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Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.

Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.

Posttraumatic stress disorder (PTSD) is a common consequence of traumatic injury, yet certain biological factors contributing to PTSD are poorly understood. The gut microbiome may influence mental health outcomes, but its role in heterogeneous PTSD presentations requires elucidation. Bacterial composition was examined in adults 2–4 years post-trauma with probable PTSD (n = 24) versus trauma-exposed controls without probable PTSD (n = 24). 16S rRNA sequencing and bioinformatic tools assessed microbial diversity and abundance. Relationships between taxa and PTSD symptom clusters were evaluated. No differences were found in overall microbial community structure between groups. The probable PTSD group exhibited significantly reduced Actinobacteriota and increased Verrucomicrobiota phylum abundance compared to controls. Specific taxa showed notable inverse associations with negative mood/cognition versus hyperarousal symptoms. Prevotella and Ruminococcaceae were negatively associated with negative mood but positively associated with hyperarousal. Results demonstrate microbial signatures of probable PTSD subtypes, highlighting the microbiome as a potential mediator of heterogeneous trauma psychopathology. Definition of PTSD microbial correlates provides a foundation for personalized psychobiotic interventions targeting predominant symptom profiles. • PTSD group had lower relative Actinobacteriota, higher Verrucomicrobiota compared to controls. • No differences in overall community structure, diversity, or other major phyla • Prevotella, Ruminococcaceae, Lachnospiraceae inversely related to symptom clusters. • Findings suggest microbial heterogeneity across PTSD subtypes. [ABSTRACT FROM AUTHOR]

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

Objective: The aim of this study is to comprehensively investigate the temporal dynamics of faecal gut microbiota and metabonomics in early postnatal with a focus on very low or extremely low birth weight (VLBW/ELBW) infants. Methods: We collected faecal samples from 157 VLBW/ELBW infants at three time points: days 1, 14, and 28 in a prospective cohort study. The faecal microbial diversity, abundance, composition, and metabolomic analyses were determined using 16S rRNA sequencing and liquid chromatography tandem mass spectrometry (LC-MS/MS). Microbiome functional analyses were conducted utilizing PICRUSt2. The ecological association networks were employed to investigate the interactions between gut microbiota and identify the core genus within 28 days of birth, as well as to unveil correlations between taxa and metabolites. Result: (1) The alpha diversity of gut microbiota significantly decreased from D1 to D28, accompanied by an interrupted trajectory lacking obligate anaerobes. At the phylum level, the 16S RNA sequencing results showed an increase in Proteobacteria and a decrease in Firmicutes and Bacteroidota from D1 to D28. At the genus level, there was a decrease in the relative abundance of Staphylococcus, Acinetobacter and Ureaplasma, with Klebsiella and Enterococcus emerging as the most abundant genera. (2) The analysis revealed a total of 561 metabolic markers that exhibited significant and distinct alterations between D1 and D14. (3) Ecological association networks revealed that the gut microbiota in D1 exhibited a significantly higher degree of microbial interactions compared to those in D14 and D28. Additionally, Enterococcus, Klebsiella, and Enterobacter were major contributors to the co-occurring network at these three time points. (4) Steroid hormone biosynthesis, including tetrahydrocortisone, androsterone glucuronide, androstenedione and etiocholanolone glucuronide, decreased within 28 days after birth. Conclusion: We have successfully demonstrated a significant dysbiosis in the gut microbiota and a subsequent decrease in its diversity within 4 weeks postpartum in VLBW/ELBW infants. Monitoring the gut microbiota of VLBW/ELBW infants and promptly rectifying dysbiosis in the early stages may represent a potential therapeutic strategy. [ABSTRACT FROM AUTHOR]

Microbial communities play a crucial role in the physiology of animal hosts; however, little is known about bacterial symbionts with the group cephalopods, specifically octopuses, and the function of these symbionts. The goal of this study was to determine if octopuses have a unique skin microbiome. The skin microbiome of two sympatric octopuses (Octopus vulgaris and Macrotritopus defilippi) was compared with the surrounding environment, sediment and seawater, to determine if octopus have a unique skin microbiome. High throughput sequencing of the bacterial 16S rRNA gene (V3-V4 region) amplicons was performed using an Illumina MiSeq. Sediment showed the greatest alpha diversity followed by octopus then seawater. Beta diversity revealed a difference in microbial composition between the octopus skin microbiome and sediment and seawater. While phylum Bacteroidetes appeared rare in environmental samples, it was most abundant for the octopus skin microbiome with the majority of the bacteria comprising the family Flavobacteriaceae. Proteobacteria, the largest group of bacteria, also constituted the octopus skin microbiome. Many of these groups occur on both octopus species; however, certain taxa differed in relative abundance between octopus species and may show species-specific host selection. Several bacteria that were identified for the octopus skin microbiome have been isolated from other marine animal hosts, identified as biodegraders and/ or produce pigments and squalene, or act as predators of other bacteria. These groups may play a role in defense against environmental stressors or pathogenic bacteria. This is the first study to characterize the skin microbiome in two wild sympatric octopuses. Due to the importance of bacterial symbionts, this can provide insight to the physiology, behavior, ecology, and ultimately the health of these important animals in marine environments as well as care in captive or laboratory settings. [ABSTRACT FROM AUTHOR]

In human microbiome studies, mediation analysis has recently been spotlighted as a practical and powerful analytic tool to survey the causal roles of the microbiome as a mediator to explain the observed relationships between a medical treatment/environmental exposure and a human disease. We also note that, in a clinical research, investigators often trace disease progression sequentially in time; as such, time-to-event (e.g., time-to-disease, time-to-cure) responses, known as survival responses, are prevalent as a surrogate variable for human health or disease. In this paper, we introduce a web cloud computing platform, named as microbiome mediation analysis with survival responses (MiMedSurv), for comprehensive microbiome mediation analysis with survival responses on user-friendly web environments. MiMedSurv is an extension of our prior web cloud computing platform, named as microbiome mediation analysis (MiMed), for survival responses. The two main features that are well-distinguished are as follows. First, MiMedSurv conducts some baseline exploratory non-mediational survival analysis, not involving microbiome, to survey the disparity in survival response between medical treatments/environmental exposures. Then, MiMedSurv identifies the mediating roles of the microbiome in various aspects: (i) as a microbial ecosystem using ecological indices (e.g., alpha and beta diversity indices) and (ii) as individual microbial taxa in various hierarchies (e.g., phyla, classes, orders, families, genera, species). To illustrate its use, we survey the mediating roles of the gut microbiome between antibiotic treatment and time-to-type 1 diabetes. MiMedSurv is freely available on our web server (http://mimedsurv.micloud.kr). [ABSTRACT FROM AUTHOR]

Bacterial culturomics is a set of techniques to isolate and identify live bacteria from complex microbial ecosystems. Despite its potential to revolutionize microbiome research, bacterial culturomics has significant challenges when applied to human gut microbiome studies due to its labor-intensive nature. Therefore, we established a streamlined culturomics approach with minimal culture conditions for stool sample preincubation. We evaluated the suitability of non-selective medium candidates for maintaining microbial diversity during a 30-day incubation period based on 16S rRNA gene amplicon analysis. Subsequently, we applied four culture conditions (two preincubation media under an aerobic/anaerobic atmosphere) to isolate gut bacteria on a large scale from eight stool samples of healthy humans. We identified 8141 isolates, classified into 263 bacterial species, including 12 novel species candidates. Our analysis of cultivation efficiency revealed that seven days of aerobic and ten days of anaerobic incubation captured approximately 91% and 95% of the identified species within each condition, respectively, with a synergistic effect confirmed when selected preincubation media were combined. Moreover, our culturomics findings expanded the coverage of gut microbial diversity compared to 16S rRNA gene amplicon sequencing results. In conclusion, this study demonstrated the potential of a streamlined culturomics approach for the efficient isolation of gut bacteria from human stool samples. This approach might pave the way for the broader adoption of culturomics in human gut microbiome studies, ultimately leading to a more comprehensive understanding of this complex microbial ecosystem. [ABSTRACT FROM AUTHOR]

Introduction: Accumulating evidence has supported that gut microbiota and metabolite profiles play indispensable roles in the pathogenesis of colorectal cancer (CRC), which ranks as the third most common cancer and the second leading cause of cancer-related deaths worldwide. However, alterations in tumoral or circulating microbiomes in CRC remain incompletely understood. It has been well-documented that tissue or serum microbiomes with low microbial biomass could be screened by use of 2bRAD sequencing for microbiome (2bRAD-M) at the species resolution. Methods: In order to validate the microbial biomarkers distinguishing CRC and the variations in microorganisms present in serum and tumors, we performed 2bRAD-M to characterize the microbiomes in serum and cancer tissues of CRC patients with and without lymph node or liver metastasis. Results: The composition of dominated microbiota in serum was different from that of tissue samples, while the microbial community composition of tumors was similar to that of the tumor-adjacent tissues. The analysis of α-diversity and β-diversity has revealed notable variations in serum microbiota diversities in CRC patients, particularly those with liver metastasis. Multiple CRC-specific microbial species, such as Moraxella A cinereus, Flavobacterium sp001800905, and Acinetobacter albensis, were identified in serum. Complicated functions and KEGG pathways were also confirmed in CRC according to the metastasis status. Discussion: This study has found significant alterations in the microbial compositions and diversities in CRC and CRC-specific microbial species in both circulation and cancer tissues, which may serve as promising biomarkers for the screening, diagnosis and prognosis prediction of CRC. In particular, CRC-specific bacterial taxa are promising markers, holding transformative potentials in establishing personalized screening and risk stratification, refining much earlier non-invasive diagnostic approaches, and enhancing diagnostic sensitivity. [ABSTRACT FROM AUTHOR]

To promote sustainable cultivation and soil health in agriculture, urgent strategies are needed to address the challenges posed by continuous cropping for high-quality pepper production. This study investigated the impact of oats incorporation and biochar amendment in a 12-year continuous pepper cropping system. Compared with the pepper monoculture system (CK), the combination treatment of intercropping with oats and biochar amendment (T1) significantly increased the soluble solids content by 3.13% and the β-carotene content by 8.83-fold in pepper fruits (P < 0.05). The soil pH under intercropping with oats or biochar modification was comparable to that of the CK. Notably, lower soil bacterial operational taxonomic units were observed under this treatment, and soil bacterial diversity decreased consistently with pepper development, regardless of the cultivation system. In contrast, fungal diversity exhibited fluctuations under the companion oat/biochar condition, with fungal community patterns modulated throughout the pepper development process (P < 0.05). Dominant microbes such as Sphingomonas, Pseudomonas, Chrysosporium, Mortierella, and Cladosporium were identified in continuous cropping pepper soils. Kyoto Encyclopedia of Genes and Genomes metabolic profiling revealed significant effects of the cultivation type on the metabolic pathways of functional genes in soil microbial communities. Overall, the practice of planting oats and using biochar in the soils of continuously cropped pepper fields is feasible and sustains the pepper industry as an agroecosystem. [ABSTRACT FROM AUTHOR]

The present study assessed the growth and fish performance of juvenile red sea bream fed four isonitrogenous (46–48%) and isolipidic (15%) diets containing 45% fishmeal (control) and 15%, 30%, and 45% defatted black soldier fly (BSF) Hermetia illucens meal for 67 days. Subsequent analyses showed that there were no significant differences in the growth parameters, nutrient digestibility, and body composition of fish among all treatments. Although no significant difference was observed in fish growth, low growth was observed when the fish meal was totally replaced with the BSF meal. Higher alpha diversity of intestinal microbiota was observed in fish fed the BSF meal-based diet compared to that of the control. In the treatment groups fed the BSF meal, elevations in the presence of microbial genera that produce digestive enzymes, such as chitinase (Nocardia, Vibrio, Paenibacillus, Photobacterium), lipase (Paenibacillus, Photobacterium), and trypsin-like serine protease (Bacillus, Paenibacillus) and vitamin B group [biotin (Vibrio, Paenibacillus, Bacillus), cobalamin (Pseudomonas, Bacillus, Propionibacterium), and pyridoxin (Photobacterium)], were observed. We also found an increasing trend of bacteria producing antioxidative enzymes, such as superoxide dismutase and catalase (Nocardia, Pseudomonas, Photobacterium) in the BSF groups. These results suggested that the BSF meal could replace 67% of fishmeal without causing a negative impact on growth and lead to beneficial effects on the intestinal microbiota of the red sea bream. [ABSTRACT FROM AUTHOR]

Nocardioform placentitis is a poorly understood disease of equine late gestation. The presence of nocardioform, filamentous branching gram-positive bacteria, has been linked to the disease, with Crossiella equi , Amycolatopsis spp., and Streptomyces spp. being the most frequently identified bacteria. However, these bacteria are not found in all clinical cases in addition to being isolated from healthy, normal postpartum placentas. To better understand this form of placentitis, we analyzed the microbial composition in the equine placenta (chorioallantois) of both healthy postpartum (control; n = 11) and nocardioform-affected samples (n = 22) using 16S rDNA sequencing. We found a lower Shannon index in nocardioform samples, a higher Chao1 index in nocardioform samples, and a difference in beta diversity between control and nocardioform samples (p < 0.05), suggesting the presence of dysbiosis during the disease. In the majority of the NP samples (77 %), one of the following genera— Amycolatopsis , Crossiella , Lentzea , an unidentified member of the Pseudonocardiaceae family, Mycobacterium, or Enterococcus —represented over 70 % of the relative abundance. Overall, the data suggest that a broader spectrum of potential opportunistic pathogens could be involved in nocardioform placentitis, extending beyond the traditionally recognized bacteria, resulting in a similar histomorphological profile. • Non-nocardioform opportunistic pathogens may be associated with placentitis. • Nocardioform placentitis is associated with dysbiotic changes. • Nocardioform placentitis exhibits a unique microbial diversity distinct from control samples. [ABSTRACT FROM AUTHOR]

Lignocellulosic biomass is of significant industrial and scientific interest. Residues derived from different activities (agro-industrial work, food consumption, wood use, urban solid waste, etc.) and their subsequent use are key to extending circularity models to the different technological sectors that are beginning to implement circular economy cycles. Biorefineries are integrated platforms that value waste conversion into various value-added products. The generation of bioproducts derived from lignocellulosic waste (green fuels, green chemicals, and biomaterials) has promoted a shift from a fossil fuel–based economy to a more sustainable one. In addition, integrating biorefineries into the circular economy framework promotes a comprehensive approach to resource management, waste reduction, and sustainable development, which contributes to the overall resilience and efficiency of societal systems. There has been increased focus on the application of "canonical microorganisms" for residual biomass conversion, such as fungi, bacteria, and yeast. However, there is a plethora of other potential microorganisms that can be candidates for new biotechnological applications. This review aims to describe the valorization of different sources of lignocellulosic biomass in the global context, with a focus on Brazilian practice, and to emphasize how the use of microbial diversity is critical to enhancing current technologies, such as advanced liquid fuels. Finally, there is a discussion of the potential of anaerobic fungi, archaea, protists, and oomycetes as microbial product conversion technologies. [ABSTRACT FROM AUTHOR]

BACKGROUND: Cold chain distribution with multiple links maintains low temperatures to ensure the quality of meat products, whereas temperature fluctuations during this are often disregarded by the industry. The present study simulated two distinct temperatures cold chain distribution processes. Quality indicators and high‐throughput sequencing were employed to investigate the effects of temperature fluctuations on the quality and microbial diversity of beef meatballs during cold chain distribution. RESULTS: Quality indicators revealed that temperature fluctuations during simulated cold chain distribution significantly (P < 0.05) exacerbated the quality deterioration of beef meatballs. High‐throughput sequencing demonstrated that temperature fluctuations affected the diversity and structure of microbial community. Lower microbial species abundance and higher microbial species diversity were observed in the temperature fluctuations group. Proteobacteria and Pseudomonas were identified as the dominant phylum and genus in beef meatballs, respectively, exhibiting faster growth rates and greater relative abundance under temperature fluctuations. CONCLUSION: The present study demonstrates that temperature fluctuations during simulated cold chain distribution can worsen spoilage and shorten the shelf life of beef meatballs. It also offers certain insights into the spoilage mechanism and preservation of meat products during cold chain distribution. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

BACKGROUND: Yangjiang douchi (YD) is a traditional fermented soybean product, which is popular in Chinese cuisine for its unique flavor. However, due to its high salt content and unstable flavor, its competitiveness in the international market is gradually weakening. Microorganisms have a key role in the production process of YD because it is a fermented food but the effect of microorganisms on the volatile compounds of YD is also not currently clear. RESULTS: In this paper, aroma compounds and microbial diversity in different fermentation stages of YD were analyzed using gas chromatography–mass spectrometry/olfactometry (GC–MS/O) and IlluminaMiseq system sequencing. A total of 78 aroma‐active compounds were detected throughout the fermentation process and they influenced the formation of flavor in YD. Fungi flora were relatively single in YD, and bacteria were rich and varied. A total of 418 species of bacteria were present during fermentation, with unclassified_Staphylococcus, Staphylococcus_kloosii, and Bacillus_velezensis_Bacillus predominating. There were 25 species of fungi at the species level, and Aspergillus minisclerotigenes (OTU 4) played a dominant role in the whole fermentation process. CONCLUSION: Staphylococcus and Bacillus in the bacterial genus were strongly correlated with most flavor compounds detected, and A. minisclerotigenes in the fungi were more relevant to flavor compounds. This research provides a theoretical basis for the enhancement of the flavor of traditional fermented douchi in China. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The microbiome is intricately linked to the development of psoriasis, serving as both a potential cause and consequence of the psoriatic process. In recent years, there has been growing interest among psoriasis researchers in exploring how psoriasis treatments affect the skin and gut microbiome. However, a comprehensive evaluation of the impact of modern treatment approaches on the microbiome has yet to be conducted. In this systematic review, we analyze studies investigating alterations in the skin and gut microbiome resulting from psoriasis treatment, aiming to understand how current therapies influence the role of the microbiome in psoriasis development. The systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. PubMed and Scopus databases were searched for eligible studies from the inception dates until July 5, 2023. Study selection, data extraction, and risk of bias assessment were carried out by three overlapping pairs of reviewers, resolving any disagreements through consensus. Our analysis of various treatments, including biologics, conventional medications, phototherapy, and probiotics, reveals significant shifts in microbial diversity and abundance. Importantly, favorable treatment outcomes are associated with microbiota alterations that approach those observed in healthy individuals. While the studies reviewed exhibit varying degrees of bias, underscoring the need for further research, this review supports the potential of microbiome modulation as both a preventive and therapeutic strategy for psoriasis patients. The findings underscore the importance of personalized therapeutic approaches, recognizing the profound impact of treatment on the microbiome. They also highlight the promise of probiotics, prebiotics, and dietary interventions in psoriasis management. [ABSTRACT FROM AUTHOR]

Characteristics of microbiome of the pig's digestive tract play an important role in the animal's physiology, including metabolism, nutrient processing, the body's immune response, and disease resistance. This study aims to analyze the abundance and diversity of microorganisms (pathogenic and non-pathogenic) from the digestive system of pigs on farms in Tangerang District. The samples used in this research were pig feces from 43 pig farms in Tangerang District. Then DNA extraction was carried out using the Zymo Quick-DNA Fecal/Soil Microbe Kit according to manufacturing procedures. Sequencing was performed using an MGI DNBSEQ-G50 machine with a DNBSEQG50RS High-throughput sequencing set (FCL PE100) according to manufacturing procedures. The quality of fastq files was evaluated with FastQC. Taxonomic classification of the processed sequences was performed using Diamond, followed by MEGAN6. The microbiome of the pig's digestive system was dominated by bacteria (85%) with the taxonomic profile at the phylum level of abundance dominated by Firmicutes (84.46%) and Bacteroidetes (9.11%). Abundance at the genus level was dominated by Enterococcus (20.44%) and Clostridium (10.31%), and at the species level it was dominated by Escherichia coli (4.92%) and Levilactobacillus brevis (4.84%). There were 10 species of pathogenic bacteria detected, with E. coli showing the highest relative abundance (4.92%). Changes in the gut microbiome play an important role in the physiology of animal health and disease. In addition, the pathogenic bacteria detected not only affect the health and productivity of pigs but also have the potential to threaten public health. [ABSTRACT FROM AUTHOR]

Little is known about the effect of gut microbial and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) carriage, particularly in the general population. The aim of this study was to identify microbiota signatures uniquely correlated with ESBL-E carriage. We conducted a case–control study among individuals seeking care at the Sexual Health Clinic or Department of Infectious and Tropical Diseases, Saint-Antoine Hospital, Paris, France. Using coarsened exact matching, 176 participants with ESBL-carriage (i.e. cases) were matched 1:1 to those without ESBL-carriage (i.e. controls) based on sexual group, ESBL-E prevalence of countries travelled in <12 months, number of sexual partners in <6 months, geographic origin, and any antibiotic use in <6 months. 16S rRNA gene amplicon sequencing was used to generate differential abundances at the genus level and measures of α- and β-diversity. Participants were mostly men (83.2%, n = 293/352) and had a median age of 33 years (interquartile range: 27–44). Nine genera were found associated with ESBL-E carriage: Proteus (p < 0.0001), Carnobacterium (p < 0.0001), Enterorhabdus (p 0.0079), Catonella (p 0.017), Dermacoccus (p 0.017), Escherichia/Shigella (p 0.021), Kocuria (p 0.023), Bacillus (p 0.040), and Filifactor (p 0.043); however, differences were no longer significant after Benjamini–Hochberg correction (q > 0.05). There were no differences between those with versus without ESBL-E carriage in measures of α -diversity (Shannon Diversity Index, p 0.49; Simpson Diversity Index, p 0.54; and Chao1 Richness Estimator, p 0.16) or β -diversity (Bray–Curtis dissimilarity index, p 0.42). In this large carefully controlled study, there is lacking evidence that gut microbial composition and diversity is any different between individuals with and without ESBL-E carriage. [ABSTRACT FROM AUTHOR]

One of the greatest challenges in poultry production is maintaining intestinal mucosal barrier integrity and gut microbiota balance. Safe alternative antimicrobials that can regulate the microbial community through animal feed have been the subject of research in poultry production. This study evaluated the effect of Mentha piperita and Melaleuca alternifolia essential oils (EOs) on the gut microbiome and morphometry of broiler quails under normal feeding conditions. The gut microbiome was studied using a completely randomized design consisting of 4 treatments, namely control, bacitracin zinc, and the Eos M. piperita and M. alternifolia, with 8 repetitions and 7 quails per treatment, totaling 224 quails from 1 to 42 days old. The intestinal contents of the slaughtered quails were collected to evaluate the gut microbiome profile of their digestive tract. Gut morphometry was analyzed using a completely randomized factorial design, with four experimental rations for three intestinal sections (4x3) and five replications. The variables studied were villus surface area and height, crypt depth, villus height to cryptdepth ratio (VH:CD), villus-crypt ratio (V:C), villus width to height ratio (VW:H), and height of the intestinal epithelium and musculature. M. alternifolia (50 mg/kg of feed) in the diet of broiler quails improved gut morphometry, similar to the results obtained with bacitracin zinc. This EO also altered the gut microbiome of quails and reduced pathogenic bacterial diversity. [ABSTRACT FROM AUTHOR]

This study was designed to recover representative culturable actinomycetes from the Atacama Desert, and to detect their ability to promote plant growth under drought conditions. Environmental samples were taken from three Atacama Desert habitats, namely, from the Aguas Calientes, Lomas Bayas and Yungay core regions. With one exception higher actinomycete counts were obtained when isolation media were inoculated with mineral particles than with corresponding aliquots of serial dilution. Comparative 16S rRNA gene sequencing showed that representative isolates belonged to thirteen genera including putative novel Blastococcus, Kocuria, Micromonospora, Pseudonocardia, Rhodococcus and Streptomyces species. Representative isolates produced indole-3-acetic acid, siderophore and solubilized phosphate as well as displaying an ability to grow under drought conditions. In conclusion, the current findings open up exciting prospects for the promising potential of actinomycetes from the Atacama Desert to be used as bioinoculants to promote plant growth in arid and semi-arid biomes. [ABSTRACT FROM AUTHOR]

Bioaerosol emitted in university biological laboratories may exert adversely effects on employees and students. The occupational health and safety have been given much importance. This study aimed to monitor the risk of bioaerosol formation inside a biological wastewater treatment laboratory where other biological activities were performed along with wastewater treatment using the biological method. The concentration of bacterial and fungal bioaerosols was studied, and the diversity of the air microbiota was evaluated, using a single-stage impactor. The purpose of the Corelation research was to evaluate the effects of indoor biological activity unique to wastewater labs and building characteristics. Increased number of occupants (corelation efficient- 0.71 and 0.47 respectively) and their experimental activity related to wastewater treatment drastically elevated both mesophiles (2018 MPN·m−3) and psychrophiles (1128 MPN·m−3) concentrations in early winter, which crossed permissible limits, whereas the fungal concentration was found below the upper permissible limits (78 MPN·m−3) in same condition. The fungal bioaerosols were found to get influenced by seasonal change and humidity (highest during autumn- 406 MPN·m−3) and were not really influenced by number of occupants (corelation efficient- 0.33). This result suggests a moderate risk of bacterial bioaerosol to occupants working in wastewater treatment laboratory. These findings may contribute to promotion and implementation of indoor environment safety at educational institute and may help in formation of policy to regulate indoor bioaerosol levels. [ABSTRACT FROM AUTHOR]

Despite advances in treatment strategies, breast cancer (BC) remains one of the most prevalent cancers worldwide. Recent studies implicate the gut microbiome as a potential risk factor for BC development. Alterations in gut microbial diversity resulting in dysbiosis have been linked to breast carcinogenesis by modulating host immune responses and inflammatory pathways, favoring tumorigenesis and progression. Moreover, gut microbiota populations are different between women with BC vs those that are cancer free, further implicating the role of the gut microbiome in cancer development. This alteration in gut microbiota is also associated with changes in estrogen metabolism, which strongly correlates with BC development. Gut microbiota that express the enzyme β-glucuronidase (GUS) may increase estrogen bioavailability by deconjugating estrogen-glucuronide moieties enabling reabsorption into circulation. Increased circulating estrogens may, in turn, drive estrogen receptor–positive BC. GUS-expressing microbiota also affect cancer therapy efficacy and toxicity by modifying glucuronide-conjugated drug metabolites. Therefore, GUS inhibitors have emerged as a potential antitumor treatment. However, the effectiveness of GUS inhibitors is still exploratory. Further studies are needed to determine how oral endocrine-targeting therapies may influence or be influenced by the microbiota and how that may affect carcinogenesis initiation and tumor recurrence. [ABSTRACT FROM AUTHOR]

This study investigates the potential of leaf and various organic waste composts as bioorganic fertilizers using 16S rRNA metagenomics. The microbial richness and diversity analysis, employing alpha and beta diversity indices, reveal substantial variations influenced by organic substrates during composting. The leaf compost had a high total OTU (70,554) but low microbial diversity (Chao 1 index = 272.27). The kitchen waste compost had the highest microbial diversity (Chao 1 index = 429.18). Positive correlations between microbial biomass, diversity, and compost quality highlighted the pivotal role of microbial activity. The beneficial genera identified across all the bio-composts were Lactobacillus, Leuconostoc, Sphingobacterium, Paenibacillus, Pseudomonas, and Clostridium. Some pathogenic genera were also detected in all the composts analyzed, viz. Prevotella, Agrobacterium, Fusobacterium, and Streptococcus. Nonetheless, the ratio of beneficial to the pathogenic genera was generally high in all compost, highlighting the enrichment with beneficial microorganisms. The leaf compost demonstrated the highest proportion of beneficial genera, about 92%, indicating significant bio-fertilizing potential, with a low % level of pathogenic genera of about 3%. Thus, the leaf compost has excellent potential to be used as a bioorganic fertilizer. Understanding the microbial composition of organic waste composts is crucial for its application as bio-fertilizer for promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio‐indicators of aged polluted drains. [ABSTRACT FROM AUTHOR]

Background: Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology. Methods: Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups. Results: Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism. Conclusions: These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms. [ABSTRACT FROM AUTHOR]

Background: Maternal diet quality and quantity have significant impacts on both maternal and fetal health and development. The composition and function of the maternal gut microbiome is also significantly influenced by diet; however, little is known about the impact of gestational nutrient restriction on the bovine maternal microbiome during early gestation, which is a critical stage for maternal microbiome-mediated fetal programming to take place. The objective of the present study was to evaluate the impacts of diet restriction and one-carbon metabolite (OCM) supplementation during early gestation on maternal ruminal, vaginal, and blood microbiota in cattle. Thirty-three beef heifers (approx. 14 months old) were used in a 2 × 2 factorial experiment with main factors of target gain (control [CON]; targeted 0.45 kg/d gain vs restricted [RES]; targeted − 0.23 kg/d gain), and OCM supplementation (+ OCM vs − OCM; n = 8/treatment; except n = 9 for RES–OCM). Heifers were individually fed, starting treatment at breeding (d 0) and concluding at d 63 of gestation. Ruminal fluid and vaginal swabs were collected on d − 2, d 35, and d 63 (at necropsy) and whole blood was collected on d 63 (necropsy). Bacterial microbiota was assessed using 16S rRNA gene (V3–V4) sequencing. Results: Overall ruminal microbiota structure was affected by gain, OCM, time, and their interactions. The RES heifers had greater microbial richness (observed ASVs) but neither Shannon nor Inverse Simpson diversity was significantly influenced by gain or OCM supplementation; however, on d 63, 34 bacterial genera showed differential abundance in the ruminal fluid, with 25 genera enriched in RES heifers as compared to CON heifers. In addition, the overall interaction network structure of the ruminal microbiota changed due to diet restriction. The vaginal microbiota community structure was influenced by gain and time. Overall microbial richness and diversity of the vaginal microbiota steadily increased as pregnancy progressed. The vaginal ecological network structure was distinctive between RES and CON heifers with genera-genera interactions being intensified in RES heifers. A relatively diverse bacterial community was detected in blood samples, and the composition of the blood microbiota differed from that of ruminal and vaginal microbiota. Conclusion: Restricted dietary intake during early gestation induced significant alterations in the ruminal microbiota which also extended to the vaginal microbiota. The composition of these two microbial communities was largely unaffected by OCM supplementation. Blood associated microbiota was largely distinctive from the ruminal and vaginal microbiota. [ABSTRACT FROM AUTHOR]

Introduction: Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrassassociated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass. Methods: We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China. Results: Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities. Conclusion: The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions. [ABSTRACT FROM AUTHOR]

Both regional species pool and local community assembly mechanism drive the microbial diversity patterns across geographical gradients. However, little has been done to separate their effects on the β diversity patterns of microbial communities involved in nitrogen (N) cycling in river ecosystems. Here, we use high‐throughput sequencing of the archaeal amoA, bacterial amoA, nirK, and nirS genes, null model, and neutral community model to distinguish the relative importance of species pool and local assembly processes for ammonia‐oxidizing and denitrifying communities in river wetlands along a latitudinal gradient in eastern China. Results indicated that the β diversity of the nirS‐type denitrifying community co‐varied with γ diversity and environmental heterogeneity, implying that regional species pool and heterogeneous selection explained variation in β diversity. However, the β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities did not correlate with γ diversity and environmental heterogeneity. The continuous hump distribution of β deviation along the latitudinal gradient and the lower species dispersal rate indicated that the dispersal limitation shaped the variation in β diversity of ammonia‐oxidizing and nirK‐type denitrifying communities. Additionally, biotic interactions drove ammonia‐oxidizing and nirS‐type denitrifying communities by influencing species co‐occurrence patterns. Our study highlights the importance of regional species pool and local community assembly processes in shaping geographical patterns of N‐cycling microorganisms and extends knowledge of their adaptability to a continuously changing environment on a large scale. [ABSTRACT FROM AUTHOR]

Morocco is a leading citrus producer with a Mediterranean climate and fertile soil. The diversity of microbial communities is a subtle indicator of this fertility and lends insights into soil function and sustainability. We compare the soil microbiome under oranges in the Taroudant and Béni Mellal regions: 90 samples were analysed by genetic sequencing using Illumina MiSeq. Several groups of microorganisms play a key role in soil health, tree growth, and the production of good quality fruit. Proteobacteria dominate the bacterial phyla, Ascomycota the fungal phyla, but ANOVA reveals a highly significant difference between the two studied areas (R = 0.164, p = 0.001) in terms of bio-sustainability and microbiome. According to the Similarity Percentage Test, the Taroudant region is characterised by high biodiversity, contributing 55% to the other parameters, whereas Béni-Mellal region exhibits high resistance of microbial communities, contributing 43% to the other parameters. [ABSTRACT FROM AUTHOR]

Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above‐ground (vegetation) and below‐ground factors (soil properties), which together create habitat‐specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode‐associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi‐arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode‐associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. Mycobacterium, Candidatus Cardinium) highlighting potentially new species‐specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above‐ and below‐ground effects to assess community structure in terrestrial habitats, and how fine‐scale analyses are critical for understanding patterns of host‐associated microbiomes. [ABSTRACT FROM AUTHOR]

Background: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney. Results: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus. Conclusions: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column. [ABSTRACT FROM AUTHOR]

The maternal pregnancy microbiome (including genitourinary and gut) has been linked to important pregnancy/birth and later childhood health outcomes. However, such sampling as part of large population cohort studies is logistically and financially challenging. Many countries routinely collect vaginal or vaginal-rectal swabs in late pregnancy for Group B Streptococcus (GBS) screening, but their utility for population-based research is still unclear. As part of planning for the Generation Victoria population-based cohort study beginning in pregnancy, we assessed the utility and reliability of residual clinical GBS vaginal/vaginal-rectal swabs for generating late pregnancy microbiome data. We carried out a two-phased pilot study. Phase one assessed the level of microbial diversity apparent in 'residual' clinical vaginal/vaginal-rectal swabs post clinical testing and storage for 7–10 days at 4 °C (routine clinical practice). Phase two directly assessed the impact of storage time and temperature on the microbial composition of vaginal/vaginal-rectal swabs collected specifically for research purposes. The microbiota composition in the 'residual' clinical swabs aligned with published studies. The 'research' swabs, stored at 4 °C for up to ten days, showed minimal changes in microbiota profile, compared to swabs examined on the day of collection. In contrast, significant variation in diversity was seen in swabs stored at room temperature for up to 48 h. Residual clinical material from swabs collected primarily for GBS screening in late pregnancy represent a reliable and abundant source of material for assessing the late pregnancy maternal microbiome for research purposes. This represents a low-burden opportunity for population-representative pregnancy studies to assess the potential of late pregnancy microbiome for prediction and understanding maternal and child health outcomes. [ABSTRACT FROM AUTHOR]

Cigars and cigarillos are emerging as popular tobacco alternatives to cigarettes. However, these products may be equally harmful to human health than cigarettes and are associated with similar adverse health effects. We used 16S rRNA gene amplicon sequencing to extensively characterize the microbial diversity and investigate differences in microbial composition across 23 different products representing three different cigar product categories: filtered cigar, cigarillo, and large cigar. High throughput sequencing of the V4 hypervariable region of the 16 s rRNA gene revealed 2124 Operational Taxonomic Units (OTUs). Our findings showed that the three categories of cigars differed significantly in observed richness and Shannon diversity, with filtered cigars exhibiting lower diversity compared to large cigars and cigarillos. We also found a shared and unique microbiota among different product types. Firmicutes was the most abundant phylum in all product categories, followed by Actinobacteria. Among the 16 genera shared across all product types were Bacillus, Staphylococcus, Pseudomonas, and Pantoea. Nine genera were exclusively shared by large cigars and cigarillos and an additional thirteen genera were exclusive to filtered cigars. Analysis of individual cigar products showed consistent microbial composition across replicates for most large cigars and cigarillos while filtered cigars showed more inter-product variability. These findings provide important insights into the microbial diversity of the different cigar product types. [ABSTRACT FROM AUTHOR]

In recent years, the salmon farming industry has grown significantly worldwide, and in the Faroe Islands, it has become a major industry with an annual production of over 94,000 tonnes, yielding 24% of the GDP. According to environmental regulations, the ocean floor is monitored during every production cycle at all farming sites, involving macrofaunal, sensory, and chemical analyses. However, the impact of farming activity on microorganisms in the Faroe Islands remains unknown. This study aimed to assess the impact of Atlantic salmon farming on benthic microbial communities, giving a better understanding of the effects on the foundation of the benthic food web and to assess if these are more prone to environmental impact than traditional macrofaunal biomonitoring. Sediment cores were sampled along a transect from directly below the salmon cages to a background reference site. The sampling occurred prior to the release of salmon into the cages ('before stocking') and immediately before the salmon were harvested ('peak biomass'). The 16S rRNA (V4-V5) gene was sequenced on an Illumina MiSeq from our sediment samples at the surface, 3 cm, and 10 cm depth. Significant shifts in microbial community composition were observed between 'before stocking' and 'peak biomass', as well as between different depth layers. Microbial diversity increased with increasing distance from the cages and was at its highest 'before stocking', indicating a significant impact of the salmon farming on the microbial community structure. In contrast to the regularly executed environmental monitoring, the results from this study showed an impact on the sediments by the salmon farming, underlining the powerful alternative of DNA-metabarcoding when biomonitoring an aquaculture area. [ABSTRACT FROM AUTHOR]

One of the primary challenges in the spread of infectious diseases is the consumption of poorly or untreated water, which is increasingly being used due to the growth of different human activities and the effect of urbanization on freshwater sources,which are often used for consumption purposes. The determination of pathogenic bacteria in freshwater rivers influenced by anthropogenic activities allows for the assessment of the impact these factors have on water quality. Thus, the purpose of this study was to identify the diversity of pathogenic bacteria and virulence genes in the UraimRiver in the northern region of Brazil. For this purpose, surface water was collected from five points with varying degrees of anthropogenic impact along the Uraim River. In situ measurements of physicochemical components were conducted, and metagenomic analysis was used for the identification of pathogenic bacteria and virulence genes. Regarding the physicochemical parameters, variabilitywas observed among the different analysis points, as well as diversity among bacteria and virulence genes. Notably, enterobacteria and the ESKAPE group were highlighted among the bacteria, with significant negative associations found between dissolved oxygen and the diversity of virulence genes and between deforestation and population density withthepresenceofESKAPEgroupbacteria. [ABSTRACT FROM AUTHOR]

Background: Tuberculosis (TB), a major cause of disease and antimicrobial resistance, is spread via aerosols. Aerosols have diagnostic potential and airborne-microbes other than Mycobacterium tuberculosis complex (MTBC) may influence transmission. We evaluated whether PneumoniaCheck (PMC), a commercial aerosol collection device, captures MTBC and the aeromicrobiome of people with TB. Methods: PMC was done in sputum culture-positive people (≥ 30 forced coughs each, n = 16) pre-treatment and PMC air reservoir (bag, corresponding to upper airways) and filter (lower airways) washes underwent Xpert MTB/RIF Ultra (Ultra) and 16S rRNA gene sequencing (sequencing also done on sputum). In a subset (n = 6), PMC microbiota (bag, filter) was compared to oral washes and bronchoalveolar lavage fluid (BALF). Findings: 54% (7/13) bags and 46% (6/14) filters were Ultra-positive. Sequencing read counts and microbial diversity did not differ across bags, filters, and sputum. However, microbial composition in bags (Sphingobium-, Corynebacterium-, Novosphingobium-enriched) and filters (Mycobacterium-, Sphingobium-, Corynebacterium-enriched) each differed vs. sputum. Furthermore, sequencing only detected Mycobacterium in bags and filters but not sputum. In the subset, bag and filter microbial diversity did not differ vs. oral washes or BALF but microbial composition differed. Bags vs. BALF were Sphingobium-enriched and Mycobacterium-, Streptococcus-, and Anaerosinus-depleted (Anaerosinus also depleted in filters vs. BALF). Compared to BALF, none of the aerosol-enriched taxa were enriched in oral washes or sputum. Interpretation: PMC captures aerosols with Ultra-detectable MTBC and MTBC is more detectable in aerosols than sputum by sequencing. The aeromicrobiome is distinct from sputum, oral washes and BALF and contains differentially-enriched lower respiratory tract microbes. [ABSTRACT FROM AUTHOR]

Objective: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer. Methods: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed. Results: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001). Conclusion: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions. [ABSTRACT FROM AUTHOR]

The kiwifruit industry typically uses commercial pollen for artificial pollination. However, during the collection of male flowers and pollen production, pollen can be easily contaminated by pathogenic bacteria that cause diseases such as canker and flower rot. Consequently, it is crucial to understand the structure of the pollen microbial community. This study employed Illumina high-throughput sequencing technology to analyze the fungal and bacterial composition in pollen samples from various regions in Shaanxi Province. Concurrently, potential pathogenic strains were isolated using traditional microbial isolation and cultivation techniques, and their molecular identification was performed through 16S rDNA sequence analysis. A tieback test was conducted on healthy branches to verify the pathogenicity of the strains. The results revealed a rich diversity of fungi and bacteria in kiwifruit pollen. At the phylum level, pollen fungi were mainly distributed in Ascomycota, and bacteria were mainly distributed in Proteobacteria and Firmicutes. The dominant fungal genera were Mycosphaerella, Aspergillus, and Cladosporium; the dominant bacterial genera were Weissella, Pantoea, Enterobacter, and Pseudomonas, respectively. Additionally, both Erwinia persicina and Pseudomonas fluorescens, isolated from pollen, exhibited high pathogenicity toward healthy kiwifruit branches. These findings contribute to a deeper understanding of the microbial diversity in commercial kiwifruit pollen used for mass pollination. [ABSTRACT FROM AUTHOR]

Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum, and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum, and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms. [ABSTRACT FROM AUTHOR]

Mangrove forests are fundamental coastal ecosystems for the variety of services they provide, including green-house gas regulation, coastal protection and home to a great biodiversity. Mexico is the fourth country with the largest extension of mangroves of which 60% occurs in the Yucatan Peninsula. Understanding the microbial component of mangrove forests is necessary for their critical roles in biogeochemical cycles, ecosystem health, function and restoration initiatives. Here we study the relation between the microbial community from sediments and the restoration process of mangrove forests, comparing conserved, degraded and restored mangroves along the northern coast of the Yucatan peninsula. Results showed that although each sampling site had a differentiated microbial composition, the taxa belonged predominantly to Proteobacteria (13.2–23.6%), Desulfobacterota (7.6–8.3%) and Chloroflexi (9–15.7%) phyla, and these were similar between rainy and dry seasons. Conserved mangroves showed significantly higher diversity than degraded ones, and restored mangroves recovered their microbial diversity from the degraded state (Dunn test p-value Benjamini-Hochberg adjusted = 0.0034 and 0.0071 respectively). The structure of sediment microbial β-diversity responded significantly to the mangrove conservation status and physicochemical parameters (organic carbon content, redox potential, and salinity). Taxa within Chloroflexota, Desulfobacterota and Thermoplasmatota showed significantly higher abundance in degraded mangrove samples compared to conserved ones. This study can help set a baseline that includes the microbial component in health assessment and restoration strategies of mangrove forests. [ABSTRACT FROM AUTHOR]

In recent years, microbial inoculants have showed a great potential to replace chemical fertilizers as a new generation of soil amendment agents, however, the understanding of their effects on nutrient cycling within plants and rhizosphere microbial diversity are still limited. In this study, the rhizosphere growth-promoting bacteria MQB12 was used to inoculate Vigna radiata to evaluate the effects of external inoculants on plant transcriptomics and rhizosphere soil microbial diversity. Enrichment analysis using GO and KEGG revealed significant enrichment in DNA-binding transcription factor activity, transcriptional regulatory factor activity, and phenylpropanoid biosynthesis among the differentially expressed genes. MQB12 inoculation positively responded to phosphorus starvation response, increased the expression of phosphorus starvation response genes (PHT/PAP), enhanced the synthesis of ethylene and salicylic acid to cope with external stress, and improved the expression of plant disease resistance genes to strengthen the disease resistance of plants to pathogens. At the same time, microbial diversity analysis further revealed the positive effect of MQB12 inoculum. MQB12 inoculum enriched beneficial flora, improved flora abundance, changed the structure and diversity of V. radiata rhizosphere microbial community, enhanced the interconnections between the flora, and positively promoted growth. MQB12 was found to adjust the microflora of the rhizosphere, which subsequently changed the environment for plant colonization. This change led to the enrichment of beneficial bacteria and removal of pathogenic bacteria, which positively affected the internal pathways of plants. Additionally, changes in gene expression levels of plants resulted in the formation of different phenotypes and various metabolites, further influencing the formation of rhizosphere microbial communities through close contact between roots and soil. This study provides new insights into the effects of microbial agents on plant growth and root environment construction and is conducive to the further development and application of microbial agents. [ABSTRACT FROM AUTHOR]

Objective: This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis. Methods: A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis. Results: The overall 28-day mortality rate was 37.7% in severe pneumonia. Nonsurvival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial α and β diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera. Conclusion: Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings. [ABSTRACT FROM AUTHOR]

Vermicomposting utilizes the synergistic effect of earthworms with microorganisms to accelerate the stabilization of organic matter in biowastes. Nevertheless, the exact mechanism behind the maturity of vermicompost and the growth of earthworms exposed to biochar of varying particle sizes remains unclear. This study presents an investigation of the effect of biochar particle size on earthworm (Eisenia fetida) survival, microbial diversity, and the quality of vermicompost products. To address these issues, pelletized dewatered sludge samples from a municipal sewage treatment plant were amended with pine-based biochar with particle sizes of 1–2 mm, 25–75 μm, 200 nm, and 60 nm as the substrate for vermicomposting. This study revealed that the addition of millimeter-scale biochar and micron-scale biochar significantly promoted the degradation of organic matter since the organic matter in the treatment with 1–2 mm biochar at the end of the vermicomposting experiment decreased by 12.6%, which was equivalent to a 1.9-fold increase compared with that of the control. Excessive nanopowdering of nanobiochar significantly affected the survival of earthworms and led to 24.4–33.3% cumulative mortality, while millimeter-scale (mm) biochar and micron-scale (μm) biochar achieved zero mortality. The findings of this study could be used for evaluating the potential impact of nanoscale biochar to earthworms and guiding biochar-augmented vermicomposting. Highlights: The addition of 1–2 mm biochar resulted in a 1.9-fold greater reduction in organic matter compared to the control group. The introduction of 25–75 μm biochar led to a significant 94% increase in earthworm cocoons. The cumulative mortality rates of 200 nm and 60 nm biochar amendment reached peaks of 33.3% and 24.4% at first week, respectively. Earthworms excrete mucus that effectively removes attached nanobiochar. [ABSTRACT FROM AUTHOR]

Background: Psoriasis is a chronic skin condition affected by genetic and environmental factors. Changes in the skin microbiome may affect the immune system and skin barrier functions, thereby contributing to the development and progression of psoriasis. The scalp, which is a common site for psoriasis, is often resistant to therapy. Although several studies have investigated the scalp microbiome, analyses focusing on both bacteria and fungi remain scarce. Methods: We examined the scalp microbiomes of 11 patients with psoriasis complicated with scalp lesions and categorized them according to their Psoriasis Area Severity Index (PASI) scores. The bacterial and fungal data were analyzed using QIIME2 pipeline version 2021.04 and the UNITE database version 8.3, respectively. Results: The Shannon indices for mild (2 patients), moderate (4 patients), and severe (5 patients) groups were 0.97, 1.38, and 1.88, respectively. A significant correlation was observed between increased mycobiome diversity and disease severity (p = 4.07 × 10−5, Spearman's correlation: 0.9269). Compared with the mild and moderate groups, the severe group exhibited a higher abundance of Malassezia globosa. Pseudomonas and Staphylococcus were, respectively, more prevalent in the moderate and severe groups than in the mild group. Conclusions: This study highlights the potential role of increased fungal diversity and specific microbial compositions in the severity of scalp psoriasis, suggesting a possible avenue for targeted therapeutic interventions. [ABSTRACT FROM AUTHOR]

There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3–V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease. [ABSTRACT FROM AUTHOR]

Grasslands are integral to maintaining biodiversity and key ecosystem services and are under threat from climate change. Plant and soil microbial diversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, it remains virtually unknown whether plant and soil microbial diversity explain a unique portion of total variation or shared contributions to supporting multifunctionality across global grasslands. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that plant and soil microbial diversity independently predict a unique portion of total variation in above- and belowground functioning, suggesting that both types of biodiversity complement each other. Interactions between plant and soil microbial diversity positively impacted multifunctionality including primary production and nutrient storage. Our findings were also climate context dependent, since soil fungal diversity was positively associated with multifunctionality in less arid regions, while plant diversity was strongly and positively linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands. Grasslands are integral to maintaining biodiversity and key ecosystem services under climate change. This study combines a global survey of 101 grasslands with a novel microcosm experiment to show that plant and soil microbial diversity independently predict a unique portion of variation in above- and below-ground functioning. [ABSTRACT FROM AUTHOR]

Simple Summary: Rodents, as the most abundant group of mammals, offer a unique opportunity to study the relationship between diet and host gut microecology. In this study, we focused on two species of the genus Myospalax in the Eurasian steppes in China: M. psilurus and M. aspalax. These specialized herbivorous rodents have adapted to a subterranean lifestyle and exhibit distinct dietary choices. Our study aimed to investigate how their diet composition is related to their gut microbial communities and whether there are unique indicator species for their gut microecology. Using 16S amplicon technology and macro-barcoding technology, we analyzed the gut bacterial communities and diet composition of the two zokor species. We found that M. psilurus had a higher diversity of gut microbial bacterial communities compared to M. aspalax. The two species also possessed different gut bacterial indicator species, with unique relationships between their diet and gut microbes. Our results provide new insights into the adaptation of zokors to long-term subterranean life and shed light on their cellulose degradation abilities and ecological niches. As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: Recent studies have shown a correlation between piglet diarrhea and the gut microbiota. However, the precise mechanism by which intestinal microorganisms and their metabolites influence diarrhea in weaned piglets remains unclear. This study explored differences in the gut microbiota and associated metabolites between healthy and diarrheic-weaned piglets using macrogenomic and metabolomic analyses. We identified microorganisms that differed markedly between the two groups. We noticed that the number and abundance of Bacteroidaceae bacterium were strongly negatively correlated with diarrhea in weaned piglets, whereas Caudoviricetes exhibited a strong positive correlation. Our screening for markedly different metabolites such as carnosine, pantothenic acid, pyridoxal, methylimidazoleacetic acid, indole-3-acetaldehyde and 5-hydroxyindoleacetic acid, along with the identification of metabolite-related metabolic pathways like tryptophan and vitamin B6 metabolism, identified important pathways associated with gut microbiota dysbiosis caused by post-weaning diarrhea in piglets. Conjoint analysis revealed that a substantial increase in the number and abundance of Caudoviricetes, coupled with a decrease in the number and abundance of Bacteroidaceae bacterium could potentially serve as microbial markers of post-weaning diarrhea. Recent studies have shown a correlation between piglet diarrhea and the gut microbiota. However, the precise mechanism by which intestinal microorganisms and their metabolites influence diarrhea in weaned piglets remains unclear. This study explored differences in the gut microbiota and associated metabolites between healthy and diarrheic-weaned piglets using macrogenomic and metabolomic analyses. The histomorphological results showed that diarrheic piglets had shorter jejunal and ileal villi, some of which were shed, compared to healthy piglets. Substantial differences in gut microbial diversity and metabolites were also observed, with Bacteroidaceae bacterium and Caudoviricetes being the main differential organisms that were strongly correlated with host status. Microbial functions, mainly the metabolism of carbohydrates, glycans, lipids, and amino acids, as well as related enzyme activities, were substantially different. The major differential metabolites were carnosine, pantothenic acid (vitamin B5), pyridoxal, methylimidazoleacetic acid, indole-3-acetaldehyde, and 5-hydroxyindoleacetic acid. These metabolites were enriched in beta-alanine, histidine, tryptophan, and vitamin B6 metabolism, and in the pantothenate and CoA biosynthesis pathways. Combined macrogenomic and metabolomic analyses revealed that carnosine, vitamin B5, and pyridoxal were negatively correlated with Caudoviricetes; methylimidazoleacetic acid, indole-3-acetaldehyde, and 5-hydroxyindoleacetic acid were positively correlated with Caudoviricetes. Whereas carnosine and vitamin B5 were positively correlated with Bacteroidaceae bacterium, 5-hydroxyindoleacetic acid was negatively correlated. The decreased abundance of Bacteroidaceae bacterium and the increased abundance of Caudoviricetes and related metabolites likely contribute to post-weaning diarrhea in piglets. Therefore, the abundance of Bacteroidaceae bacterium and Caudoviricetes can likely serve as potential markers for identifying and preventing diarrhea in post-weaning piglets. [ABSTRACT FROM AUTHOR]

Manipulating the rhizosphere microbiome to enhance plant stress tolerance is an environmentally friendly technology and a renewable resource to restore degraded environments. Here we suggest a sustainable bioremediation strategy on the example of Stebnyk mine tailings storage. We consider Salicornia europaea rhizosphere community, and the ability of the phytoremediation plant Salix viminalis to recruit its beneficial microbiome to mediate the pollution stress at the Stebnyk mine tailings storage. The tailings contain large amounts of brine salts and heavy metals that contaminate the ground water and surrounding areas, changing soil biogeochemistry and causing increased erosion. The species richness of the endophytic bacterial community of S. viminalis roots was assessed based on observed OTUs, Shannon-InvSimpson, and evenness index. Our results obtained using the plant-based enrichment strategy show that biodiversity was decreased across the contamination zones and that S. europaea supplementation significantly increased the species richness. Our results also indicate that the number of dominating bacteria was not changed across zones in both S. europaea-treated and untreated bacterial populations, and that the decrease in richness was mainly caused by the low abundant bacterial OTUs. The importance of selecting the bioremediation strains that are likely to harbor a reservoir of genetic traits that aid in bioremediation function from the target environment is discussed [ABSTRACT FROM AUTHOR]

Accumulating evidence proves that children with autism have gastrointestinal problems. However, a significant difference in gut microbiota (GM) exists between autistic and non-autistic children. These changes in the GM may stem from several factors. Recently, researchers focused on nutritional factors, especially vitamin deficiency. Thus, our systematic review investigates the connections among autism, GM alterations, and vitamin A deficiency (VAD), by analyzing studies sourced from PubMed and Embase databases spanning from 2010 to 2022. Adhering to PRISMA guidelines, we meticulously selected 19 pertinent studies that established links between autism and GM changes or between autism and VAD. Our findings uniformly point to significant alterations in the GM of individuals with autism, indicating these changes as promising biomarkers for the disorder. Despite the consistent association of GM alterations with autism, our analysis revealed no notable differences in GM composition between individuals with autism and those experiencing VAD. This suggests that VAD, especially when encountered early in life, might play a role in the onset of autism. Furthermore, our review underscores a distinct correlation between reduced levels of retinoic acid in children with autism, a disparity that could relate to the severity of autism symptoms. The implications of our findings are twofold: they not only reinforce the significance of GM alterations as potential diagnostic markers but also spotlight the critical need for further research into nutritional interventions. Specifically, vitamin A supplementation emerges as a promising avenue for alleviating autism symptoms, warranting deeper investigation into its therapeutic potential. [ABSTRACT FROM AUTHOR]