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Background: Colorectal cancer (CRC) is a common cancer that causes millions of deaths worldwide each year. At present, numerous studies have confirmed that intestinal microbes play a crucial role in the process of CRC. Additionally, studies have shown that CRC can be divided into several consensus molecular subtypes (CMS) based on tumor gene expression, and CRC microbiomes have been reported related to CMS. However, most previous studies on intestinal microbiome of CRC have only compared patients with healthy controls, without classifying of CRC patients based on intestinal microbial composition. Results: In this study, a CRC cohort including 339 CRC samples and 333 healthy controls was selected as the discovery set, and the CRC samples were divided into two subgroups (234 Subgroup1 and 105 Subgroup2) using PAM clustering algorithm based on the intestinal microbial composition. We found that not only the microbial diversity was significantly different (Shannon index, p-value < 0.05), but also 129 shared genera altered (p-value < 0.05) between the two CRC subgroups, including several marker genera in CRC, such as Fusobacterium and Bacteroides. A random forest algorithm was used to construct diagnostic models, which showed significantly higher efficiency when the CRC samples were divided into subgroups. Then an independent cohort including 187 CRC samples (divided into 153 Subgroup1 and 34 Subgroup2) and 123 healthy controls was chosen to validate the models, and confirmed the results. Conclusions: These results indicate that the divided CRC subgroups can improve the efficiency of disease diagnosis, with various microbial composition in the subgroups. [ABSTRACT FROM AUTHOR]

The search for alternative therapies to antimicrobial growth promoters (AGP) in poultry production has gained momentum in the past years because of consumer preference and government restrictions on the use of AGP in animal production. Flavonoids are plant-derived metabolites that have been studied for their health-promoting properties that could potentially be used as an alternative to AGP in poultry. In a previous study, we showed that the inclusion of a flavonoid-rich corn cultivar (PennHFD1) in the diet improved the health of broilers undergoing necrotic enteritis. However, the mechanisms of action by which the PennHFD1-based diet ameliorated necrotic enteritis are unknown. This study describes the microbial diversity and composition of the jejunum and ileum of chickens co-infected with Eimeria maxima and Clostridium perfringens and treated with a high-flavonoid corn-based diet. Luminal content and mucosal samples from the jejunum and ileum were collected for DNA extraction, 16S rRNA amplicon sequencing and data analyses. The infection model and the dietary treatments significantly changed the alfa diversity indices (Mucosal samples: ASVs, P = 0.04; Luminal content samples: ASVs, P = 0.03), and beta diversities (Mucosal samples: P < 0.01, Luminal content: P < 0.01) of the ileal samples but not those of the jejunal samples. The microbial composition revealed that birds fed the high-flavonoid corn diet had a lower relative abundance of C. perfringens compared to birds fed the commercial corn diet. The treatments also changed the relative abundance of other bacteria that are related to gut health, such as Lactobacillus. We concluded that both the infection model and the dietary high-flavonoid corn changed the broilers' gut microbial diversity and composition. In addition, the decrease in the relative abundance of C. perfringens corroborates with a decrease in mortality and intestinal lesions due to necrotic enteritis. Collecting different segments and sample types provided a broader understanding of the changes in the gut microbiota among treatments. [ABSTRACT FROM AUTHOR]

Ionic liquids (ILs) are widely used in various fields due to their excellent properties. Despite their utility, there is limited knowledge regarding the phytotoxic properties of ILs and the mechanisms by which plants develop resistance to them. This is particularly true when considering the role of nitric oxide (NO) in response to ILs stress. Herein, we investigated the mechanism by which endogenous NO reduces the ILs’ phytotoxicity in Arabidopsis from the perspective of rhizosphere microorganisms. We investigated the impact of 1,3-dibutyl imidazole bromide (DIB) on microbial diversity and community in the rhizosphere of Arabidopsis lines with varying endogenous NO levels, using a high throughput sequencing method. DIB did not affect microbial taxon numbers, richness, or evenness; however, it did alter microbial beta diversity and community structure in the rhizosphere of Arabidopsis. Elevated endogenous NO increased fungal richness and evenness, shifted DIB’s impact on microbial community structure, and enriched more resistant species and toxin-decomposing species. These findings suggest a potential mechanism for plants to resist IL stress. Our study not only elucidates the toxicological mechanisms of ILs but also reveals the involvement of NO in plant responses to IL stress, providing valuable insights for future environmental risk assessments and mitigation strategies. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions Previous local‐scale research (within plots or landscapes) has shown that invasive plants can alter the composition and diversity of soil microbial communities, with potential feedback effects on their own invasion success. However, the broader ecological patterns of these interactions across different invasion timescales and geographic regions remain poorly understood. This study investigated whether the composition and diversity of soil microbial communities associated with Solidago canadensis (Canada goldenrod) invasion vary across both population residence times and geographic locations.South‐eastern China.Soil fungal and bacterial communities and S. canadensis.We collected rhizospheric soil of S. canadensis, nonrhizospheric soil and adjacent uninvaded soil from each of 36 populations of S. canadensis with varying residence times (8–89 years), totalling 108 samples. We extracted DNA from these samples and sequenced the V3–V4 region of the bacterial 16S rRNA gene and the ITS2 region of the fungal rDNA. We analysed the DNA sequences to assess whether variation in α‐diversity, β‐diversity, arbuscular mycorrhizal fungi (AMF) richness and the ratio of AMF to plant pathogens in the soil microbial communities varied with S. canadensis population residence time, latitude and longitude.The α‐diversity and β‐diversity of soil fungal and bacterial communities significantly varied with S. canadensis residence times, latitude and longitude. In locations where S. canadensis had been established for longer periods, there was an increase in AMF richness and a decrease in plant pathogens in the rhizospheric soil. Fungal diversity in rhizospheric soils was positively correlated with longitude, while bacterial diversity in rhizospheric and nonrhizospheric soils was positively correlated with both latitude and longitude.These findings indicate that the time since invasion and geographical location can both significantly influence the composition and diversity of soil microbial communities associated with invasive plant species. [ABSTRACT FROM AUTHOR]

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]

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties were isolated from the rhizosphere soil of tea plants. Among them, two PGPR strains with the best growth-promoting properties were then selected for the root irrigation. The PGPR treatment groups had a higher Chlorophyll (Chl) concentration in the eighth leaf of tea plants and significantly promoted the plant height and major soil elements. There were significant differences in microbial diversity and metabolite profiles in the rhizosphere between different experimental groups. PGPR improved the diversity of beneficial rhizosphere microorganisms and enhanced the root metabolites through the interaction between PGPR and tea plants. The results of this research are helpful for understanding the relationship between PGPR strains, tea plant growing, and rhizosphere soil microenvironment improvement. Moreover, they could be used as guidance to develop environmentally friendly biofertilizers with the selected PGPR instead of chemical fertilizers for tea plants. [ABSTRACT FROM AUTHOR]

This study investigates the diversity and composition of soil bacterial communities in the rhizosphere of Attapadi and Nelliyampathy, prominent hill stations in Palakkad district, Kerala, India. The persistent flooding and landslides in 2018 and 2019 significantly impacted agricultural productivity in these regions. Utilizing high-throughput 16S rRNA gene sequencing (Illumina MiSeq), we conducted a comprehensive analysis of soil samples. Correlative assessments between soil parameters and microbial relative abundance at the phylum level revealed noteworthy positive associations. Notably, nitrogen (N) exhibited a positive relation with Crenarchaeota, Chloroflexi, Actinobacteriota, and Acidobacteriota; pH correlated with Firmicutes; organic carbon (OC) with WPS-2; and phosphorous with Proteobacteria. A total of 31,402 operational taxonomic units (OTUs) were identified, with the highest feature counts observed in undisturbed soils from Attapadi (AUD) and Nelliyampathy (NUD) (13,007 and 12,915, respectively). Disturbed soils in Nelliyampathy (ND) and Attapadi (AD) displayed a substantial decline in microbial diversity and composition, harbouring 1409 and 4071 OTUs, respectively. Alpha and beta diversity indices further underscored the more severe impairment of ND soils compared to AD soils. Interestingly, a majority of ND samples were landslide-affected (four out of five), while flood-affected soils accounted for four out of six AD samples. This indicates that landslides exert a more pronounced impact on microbial diversity and composition than floods. The observed decline in microbial count, composition, and diversity, even after 2 years of the disaster, raises concerns about potential threats to agricultural output. The findings emphasize the need for corrective measures, including the incorporation of microbial inoculum, to restore soil fertility in post-disaster landscapes. [ABSTRACT FROM AUTHOR]

Proper retting process of hemp stems, in which efficient separation of cellulose fiber from the rest of the stem is promoted by indigenous microorganisms able to degrade pectin, is essential for fiber production and quality. This research aimed to investigate the effect of a pre-treatment dew retting in field of hemp stalks on the pectinolytic enzymatic activity and microbiota dynamic during lab-scale water retting process. A strong increase in the pectinase activity as well as in the aerobic and anaerobic pectinolytic concentration was observed from 14 to 21 days, especially using hemp stalks that were not subjected to a pre-retting treatment on field (WRF0 0.690 ± 0.05 U/mL). Results revealed that the microbial diversity significantly varied over time during the water retting and the development of microbiota characterizing the water retting of hemp stalks of different biosystems used in this study was affected by pre-treatment conditions in the field and water retting process and by an interaction between the two methods. Although at the beginning of the experiment a high biodiversity was recorded in all biosystems, the water retting led to a selection of microbial populations in function of the time of pre-treatment in field, especially in bacterial populations. The use of hemp stems did not subject to a field pre-treatment seems to help the development of a homogeneous and specific pectinolytic microbiota with a higher enzymatic activity in respect to samples exposed to uncontrolled environmental conditions for 10, 20, or 30 days before the water retting process. Key points: • Microbial diversity significantly varied over time during water retting. • Water retting microbiota was affected by dew pre-treatment in the field. • Retting of no pretreated hemp allows the development of specific microbiota with high enzymatic activity. [ABSTRACT FROM AUTHOR]

Though sterile diet, post‐transplantation surgery is a clinical strategy for patient care to prevent the infiltration of gut pathogens, less is known about its effects on the gut microbiome. Here, the gut microbiome dynamics of leukemia patients following a 120‐day "sterile‐normal" diet strategy posthematopoietic cell transplantation are examined. In contrast to the traditional idea, a sterile diet leads to the lowest gut microbiota diversity (p < 0.05) and short‐chain fatty acids, promoted the proliferation of potential pathogens such as Streptococcus (up by 16.93%) and Lactobacillus (up by 40.30%), and 43.32% reduction in nodes and an 85.33% reduction in edges within the microbial interaction's network. Interestingly, a normal diet allows the gut microbiome recovery and significantly promotes the abundance of beneficial bacteria. These results indicate that a sterile diet leads to a collapse of the patient's gut microbiome and promoted the proliferation of potential pathogens. This assay is a starting point for a more sophisticated assessment of the effects of a sterile diet. The work also suggests a basic principle for the re‐establishment of microbial equilibrium that supplementation of microbial taxa may be the key to the restoration of the degraded ecosystem. [ABSTRACT FROM AUTHOR]

Background: Along bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi's occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe. Results: We applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity. Conclusion: Our results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive. [ABSTRACT FROM AUTHOR]

While traditionally perceived as yield‐reducing elements in rice (Oryza sativa L.) cultivation, weed communities in paddy fields play a crucial role in the ecosystem. These communities, when selectively retained, can significantly enhance ecosystem services. This review examines the impact of various weed communities on rice in different paddy fields, their response to field nutrients, and the ecological benefits they offer. These benefits include nitrogen retention, promotion of microbial diversity, and reduction of diseases, pests, and weed proliferation. Examples of such benefits are seen in weeds like Lemna minor L. and Azolla imbricata (Roxb.) Nakai, which help in nitrogen fixation and act as biocontrol agents against harmful pests. However, current research in this area faces challenges, including the lack of intelligent and precise weed control technologies, comprehensive green control strategies, and expertise in weed management. Our findings suggest a strategic approach to weed control in paddy fields, emphasizing the importance of preserving weed species that have minimal impact on rice yields but offer significant ecological advantages. These practices can lead to grass‐mediated weed control and enhanced nutrient absorption, thereby reducing fertilizer loss. Ultimately, this approach could reduce the reliance on chemical fertilizers and herbicides in paddy fields, laying the groundwork for greener rice cultivation and sustainable agricultural practices. [ABSTRACT FROM AUTHOR]

Min pigs exhibit remarkable cold tolerance, where vitamin B1 synthesis by gut microbiota is crucial for the host's energy metabolism. However, the role of this synthesis in cold adaptation of Min pigs are not yet fully understood. This study utilized 16S rRNA amplicon and metagenomic sequencing to examine seasonal variations in the gut microbiota of Min pigs. Results indicated a significant rise in microbial diversity in winter, with the Bacteroidetes group being themost notably increased. The vitamin B1 biosynthetic pathway was significantly enriched during winter, with six significantly upregulated genes (ThiC, ThiD, ThiE, ThiG, ThiH, and ThiL) showing strong evidence of purifying selection. Among the six vitamin B1 synthesis genes significantly upregulated during winter, the increase was mainly due to a marked elevation in several sequences from specific microbial species. Binding energy analysis revealed that, except for ThiL, the average substrate binding energy of the top 10 sequences with the largest seasonal differences was significantly lower than those of the 10 sequences with the smallest differences. Furthermore, most of these sequences were uniquely prevalent in Min pigs and were not found in the homologous sequences of Duroc pigs. Bacteroidetes and Bacteroidales were identified as the primary contributors to these gene sequences. This research provides valuable insights for developing innovative cold-resistant feed and probiotics. [ABSTRACT FROM AUTHOR]

Microbial remediation has become the most promising technical means for the remediation of polycyclic aromatic hydrocarbons (PAHs) non-point source contaminated soil due to its low cost of treatment, complete degradation of pollutants, and in-situ remediation. In this study, in order to demonstrate the phenanthrene degrading microbial diversity, phenanthrene was chosen as the representative of PAHs and strains capable of degrading phenanthrene were isolated and screened from the sedimentation sludge and the bottom sludge of oil tank trucks, and high throughput sequencing was used to check the dominant strains with a good degrading effect on phenanthrene. Results showed even more than 50% of phenanthrene was degraded in all samples, the composition of PAH-degrading bacteria was diverse, and different environments constructed different functional microbial groups, which resulted in the microbial adapting to the diversity of the environment. Finally, a series of bacterial species with phenanthrene-degrading functions such as Achromobacter, Pseudomonas, Pseudochelatococcus, Bosea was enriched after nine transferring process. Overall, our study offers value information for the enrichment of functional degrading microbes of phenanthrene or other pollutants that more concern should be paid in not only the degradation rate, but also the diversity variation of microbial community composition. [ABSTRACT FROM AUTHOR]

This study utilized high-throughput sequencing to investigate endophytic bacteria diversity in halophytic plants Anabasis truncate (AT) and Anabasis eriopoda (AE) from the Aral Sea region. Following sequence processing, 356 Amplicon Sequence Variants (ASVs) were discovered. The abundance and variety of endophytic bacteria were higher in AT. Bacillota, Pseudomonadota, Actinomycetota, and Bacteroidota constituted the dominant in AE, whereas Pseudomonadota, Actinomycetota, Bacteroidota, and Chloroflexota constituted the dominant in AT. Biomarkers were identified through LEFSe analysis, showing host-specific patterns. PCoA indicated distinct bacterial community structures. Phylogenetic analysis revealed diverse endophytic bacteria, including potential novel taxa. PICRUSt2 predicted diverse functions for endophytic bacteria in halophytes, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic/tolerant bacteria. Moreover, the evolutionary relationship, metabolic capabilities, and plant beneficial potentials of the Bacillus swezeyi strains, previously isolated from the above two halophytes, were analyzed using comparative genomic and physiological analysis. The B. swezeyi strains displayed versatile environmental adaptability, as shown by their ability to use a wide range of carbon sources and their salt tolerances. B. swezeyi possessed a wide range of enzymatic capabilities, including but not limited to proteases, cellulases, and chitinases. Comparative genomic analysis revealed that despite some variations, they shared genetic similarities and metabolic capabilities among the B. swezeyi strains. B. swezeyi strains also displayed outstanding plant-growth-promoting and antagonistic potentials, offering potential solutions to the global food crisis. This study enhances our understanding of microbial diversity in halophytes on saline-alkali land in the West Aral Sea, shedding light on the halophyte microbiome and its collaboration with hosts in highly hypersaline environments. This study also provides a scientific basis for developing high-quality microbial fertilizers and implementing sustainable agricultural practices. [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]

Anaerobic soil disinfestation (ASD) is a novel, eco-friendly method to improve soil health. This method creates oxygen-free conditions by adding organic amendments as a carbon source, saturating the soil to field capacity, and then covering it with plastic. These anaerobic conditions reduce soilborne pathogens, enhance microbial diversity, and increase crop productivity. This review provides an overview of the different organic amendments used in ASD, their impact on managing soilborne pathogens, the role of beneficial microbiomes, and the challenges associated with adopting ASD. It also emphasizes the potential benefits of ASD and the innovative approach to advancing it for sustainable agriculture. [ABSTRACT FROM AUTHOR]

This study aimed to compare the microbiome profiles of patients with colorectal cancer (CRC, n =380) and colorectal adenomas (CRA, n =110) against generally healthy participants (n =2,461) from various studies. The overarching objective was to conduct a real-life experiment and develop a robust machine learning model applicable to the general population. A total of 2,951 stool samples underwent a comprehensive analysis using the in-house MetaBakery pipeline. This included various data matrices such as microbial taxonomy, functional genes, enzymatic reactions, metabolic pathways, and predicted metabolites. The study found no statistically significant difference in microbial diversity among individuals. However, distinct clusters were identified for healthy, CRC, and CRA groups through linear discriminant analysis (LDA). Machine learning analysis demonstrated consistent model performance, indicating the potential of microbiome layers (microbial taxa, functional genes, enzymatic reactions, and metabolic pathways) as prediagnostic indicators for CRC and CRA. Notable biomarkers on the taxonomy level and microbial functionality (gene families, enzymatic reactions, and metabolic pathways) associated with CRC were identified. The research presents promising avenues for practical clinical applications, with potential validation on external clinical datasets in future studies. [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]

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]

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]

Purple soil is rich in semiconducting minerals, but the impact of these minerals on soil properties and associated microbiome assemblages has received little attention. To better understand the influence of semiconducting minerals in soils, samples were collected from 4 soil classifications, including purple soil, siltstone, farmland, and new formed soil. Goethite was the main semiconducting mineral in purple soil followed by rutile and birnessite, while for siltstone, rutile was the major semiconducting mineral. Proteobacteria (77.77–98.56%) was the most prevalent phylum among all samples, with the second most abundant phylum being Cyanobacteria (purple soil and farmland) and Firmicutes (siltstone and new formed soil). According to the average path length in network analysis, purple soil showed higher species segregation, which suggested purple soil was potentially more susceptible to external interference than the other types. The relationship between microbes may be synergistic due to the positive links between microbial phyla. Rutile affected microbial composition to the greatest extent, accounting for 13.66% of the total variation in microbial assembly, while goethite (r= –0.0947) and birnessite (r = 0.0215) content were also associated with changes in microbial composition. These results demonstrated that semiconducting minerals affected the structure and potential energy utilization of soil microbial communities. [ABSTRACT FROM AUTHOR]

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments. [ABSTRACT FROM AUTHOR]

Depression is one of the most common psychiatric conditions worldwide, with an annual escalation in prevalence. The serotonin (5‐Hydroxytryptamine [5‐HT]) metabolism through the gut–brain axis has been revealed to be related to the development of depression. Our previous study demonstrated that Lactococcus lactis WHH2078 alleviated depression in mice by shaping the gut microbiome composition and 5‐HT metabolism. However, little research has explored the synergistic effects of probiotics and natural mental health‐improving products. In this study, three natural products (saffron, l‐theanine, and phosphatidylserine), either individually or in combination, were orally administrated for 4 weeks in chronic restraint stress (CRS)‐induced mice, and their depressive behaviors, hippocampal 5‐HT, and serum corticosterone were assessed. Saffron demonstrated improvement of the depressive‐like behaviors via multiple behavioral tests and reversed the declined concentration of 5‐HT and increased concentration of corticosterone. Following an initial screening, saffron was chosen to be combined with WHH2078, referred to as WHHMOOD™. Furthermore, the effects of WHHMOOD were evaluated in mice with depressive‐like behaviors. WHHMOOD reduced immobility time in the forced swimming test and tail suspension test, increased the time spent in the central area in open field test, and reduced the serum corticosterone level. Besides, WHHMOOD improved the CRS‐induced gut microbial dysbiosis by reversing gut microbial diversity and the abundances of Ligilactobacillus, Candidatus Arthromitus, and Erysipelatoclostridium. Compared to WHH2078, WHHMOOD treatment significantly increased the travel distance and hippocampal 5‐HT level in mice. In conclusion, WHHMOOD exhibited prophylactic effects on depressive‐like in CRS mice, which may act as a promising agent for improving the symptoms of depression. [ABSTRACT FROM AUTHOR]

Diverse native plant communities resist non‐native plants more than species‐poor communities, in part through resource competition. The role of soil biota in diversity–invasibility relationships is poorly understood, although non‐native plants interact with soil biota during invasions. We tested the responses of non‐native plants to soil biota generated by different native plant diversities. We applied well‐watered and drought treatments in both conditioning and response phases to explore the effects of 'historical' and 'contemporary' environmental stresses. When generated in well‐watered soils, the microbial legacies from higher native diversity inhibited non‐native growth in well‐watered conditions. In contrast, when generated in drought‐treated soils, the microbial legacies from higher native diversity facilitated non‐native growth in well‐watered conditions. Contemporary drought eliminated microbial legacy effects on non‐native growth. We provide a new understanding of mechanisms behind diversity–invasibility relationships and demonstrate that temporal variation in environmental stress shapes relationships among native plant diversity, soil biota and non‐native plants. [ABSTRACT FROM AUTHOR]

Shelter‐building insects are important ecosystem engineers, playing critical roles in structuring arthropod communities. Nonetheless, the influence of leaf shelters and arthropods on plant–associated microbiota remains largely unexplored. Arthropods that visit or inhabit plants can contribute to the leaf microbial community, resulting in significant changes in plant–microbe interactions. By artificially constructing leaf shelters, we provide evidence that shelter‐building insects influence not only the arthropod community structure but also impact the phyllosphere microbiota. Leaf shelters exhibited higher abundance and richness of arthropods, changing the associated arthropod community composition. These shelters also altered the composition and community structure of phyllosphere microbiota, promoting greater richness and diversity of bacteria at the phyllosphere. In leaf shelters, microbial diversity positively correlated with the richness and diversity of herbivores. These findings demonstrate the critical role of leaf shelters in structuring both arthropod and microbial communities through altered microhabitats and species interactions. [ABSTRACT FROM AUTHOR]

While molecular methods have begun to transform ecology, most algal biodiversity is still studied using the classical approach of identifying microalgae by light microscopy directly in sample material or using cultures. In this study, we compare both approaches (light microscopy and metagenomics as a molecular approach) using the freshwater ponds of the Eifel National Park in Germany as a case study. The ponds were found to be rich in desmids by light microscopy. A total of 299 species representing 81 genera were identified by light microscopy. While the molecular method does not currently allow species identification in most cases, we were able to identify 207 different algal genera. In total, 157 genera were detected only by metagenomics, 50 genera were found with both methods, and 31 genera were found by light microscopy, highlighting the need to continue using light microscopy in addition to a molecular approach. The metagenomics method has several advantages over the light microscopy method: (1) deeper assessment of alpha biodiversity, (2) better abundance numbers, and (3) complete coverage of all living matter. The latter is also a significant improvement over metabarcoding, as universal PCR primers are not available. [ABSTRACT FROM AUTHOR]

Legumes enhance pasture health and soil productivity by fixing atmospheric nitrogen and boosting soil microbiota. We investigated the effects of tropical pasture legumes, including butterfly pea (Clitoria ternatea), seca stylo (Stylosanthes scabra), desmanthus (Desmanthus virgatus), lablab (Lablab purpureus), and Wynn cassia (Chamaecrista rotundifolia), on the soil microbial community and buffel grass (Cenchrus ciliaris) gene expression. Additionally, we explored the impact of a phytogenic bioactive product (PHY) in the coculture system. A pot trial using soil enriched with cow paunch compost included four treatments: monoculture of buffel grass and five legume species with and without PHY supplementation and coculture of buffel grass with each legume species with and without PHY supplementation. Actinobacteriota and Firmicutes were the dominant bacterial phyla. Regardless of PHY application, the coculture of buffel grass with legumes positively influenced microbial composition and diversity. Transcriptomic analysis revealed significant gene expression changes in buffel grass shoots and roots, with each legume uniquely affecting nitrogen metabolism. Lablab and Wynn cassia exhibited similarities in modulating metabolic processes, butterfly pea contributed to mycotoxin detoxification, and desmanthus balanced cell death and growth. Seca stylo enhanced root cell growth and regeneration. These findings offer insights for optimizing legume–grass coculture systems, enhancing soil activity and promoting sustainable agriculture. [ABSTRACT FROM AUTHOR]

Irrigation and nitrogen application rates have significant effects on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how these rates affect plant–microbiome interactions and how the associated changes might impact tomato yields. In this greenhouse study conducted over two years, the effects of three irrigation levels (moderate deficit with 65–75% water holding capacity threshold, slight deficit with 75–85%, and sufficient irrigation with 85–95%) and four nitrogen application levels (60, 120, 240, and 360 kg ha−1) on tomato growth, yield, water and nitrogen productivities, and rhizosphere microbial diversities and functions were investigated. The results demonstrated that the highest tomato leaf area, dry biomass, yield, and water and nitrogen productivities were obtained under the treatment with sufficient irrigation. With increasing nitrogen application, the tomato leaf area, dry biomass, yield, and water and nitrogen productivities showed a trend of first increasing and then decreasing. Overall, the treatment (N2W3) with sufficient irrigation and 240 kg ha−1 N was associated with the highest tomato growth, yield, and water and nitrogen productivities. Moreover, optimal irrigation and nitrogen application obviously altered the structures of rhizosphere bacterial and fungal communities, particularly recruiting microbiota conferring benefits to tomato growth and nitrogen fixation—namely, Lysobacter and Bradyrhizobium. Ultimately, optimal irrigation and nitrogen application significantly increased the relative abundances of functions related to carbon, sulfur, and nitrogen metabolism, especially nitrogen fixation. In summary, optimal irrigation and fertilization enhanced tomato yield, as well as water and nitrogen productivities by increasing the nitrogen fixation functions of the rhizosphere microbiome. Our results provide significant implications for tomato cultivation in greenhouses, in terms of optimized irrigation and fertilization. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) contamination in soil has emerged as a significant challenge for agricultural production. Phytoremediation and passivation are key techniques for remediating Cd-contaminated soil. However, few studies have focused on the synergistic effects of these two techniques. In this work, the effectiveness of synergetic remediation strategies, both synchronous and asynchronous, utilizing passivation and phytoremediation techniques, was explored. The results of pot experiments and field experiments indicated that optimal remediation effects were obtained by asynchronous synergetic remediation, removing over 80% of bioavailable Cd within 14 days. Mechanistic studies conducted using XPS analysis, soil property analysis, and microbial diversity analysis confirmed that the chelation effect of SDD and soil pH value are the primary factors contributing to the effectiveness of both remediation strategies. In contrast, the variations in microbial populations are identified as the crucial factors influencing the varying outcomes of the two sequential remediation approaches. This research demonstrates that asynchronous synergistic remediation is a promising strategy for mitigating Cd contamination in soil. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal fungi (AMF) are critical for soil ecosystem services as they enhance plant growth and soil quality via nutrient cycling and carbon storage. Considering the growing emphasis on sustainable agricultural practices, this study investigated the effects of conventional and organic farming practices on AMF diversity, abundance, and ecological functions in maize, pepper, and potato-cultivated soils. Using next-generation sequencing and quantitative PCR, we assessed AMF diversity and abundance in addition to soil health indicators such as phosphorus content, total nitrogen, and soil organic carbon. Our findings revealed that, while no significant differences in soil physicochemical parameters or AMF diversity were observed across farming systems when all crop data were combined, organic farming significantly enhances AMF abundance and fosters beneficial microbial ecosystems. These ecosystems play vital roles in nutrient cycling and carbon storage, underscoring the importance of organic practices in promoting robust AMF communities that support ecosystem services. This study not only deepens our understanding of AMF's ecological roles but also highlights the potential of organic farming to leverage these benefits for improving sustainability in agricultural practices. [ABSTRACT FROM AUTHOR]

Simple Summary: Our understanding of methods by which dietary interventions can be used to modify the established gut microbiota in adult humans is rudimentary. In this intervention trial, a person's gut microbial diversity and intestinal inflammatory markers remained unchanged across four weeks of daily consumption of 80 g of wheat crackers, regardless of wheat-flour type. Consumers must understand that shifting their gut microbiota and inflammatory state with a single dietary constituent may be difficult with mild and short-term interventions. Consumption of whole-grain wheat has been associated with positive health outcomes, but it remains unclear whether different types of wheat elicit varying effects on the gut microbiome and intestinal inflammation. The objectives of this research were to investigate the effect of two whole-grain wheat flours versus refined wheat flour on the diversity of the human gut microbiota, as well as on butyrate production capacity and gastrointestinal inflammation, using one-week dietary interventions. For this study, 28 participants were recruited, with ages ranging from 18 to 55 years and a mean BMI of 26.0 kg/m2. For four weeks, participants were provided 80 g daily servings of different wheat crackers: Week A was a run-in period of crackers made from soft white wheat flour, Week B crackers were whole-grain soft white wheat flour, Week C crackers were a wash-out period identical to Week A, and Week D crackers were whole-grain soft red wheat flour. At the end of each week, participants provided fecal samples that were analyzed for markers of intestinal inflammation, including lipocalin and calprotectin, using enzyme-linked immunosorbent assays and quantitative real-time PCR. The primary outcome, gut bacterial community alpha and beta diversity, was similar across timepoints. Three taxa significantly differed in abundance following both whole-grain wheat flour interventions: Escherichia/Shigella and Acidaminococcus were significantly depleted, and Lachnospiraceae NK4A136 group was enriched. Secondary outcomes determined that protein markers of intestinal inflammation and genes related to putative butyrate production capacity were similar throughout the study period, with no significant changes. Lipocalin concentrations ranged from 14.8 to 22.6 ng/mL while calprotectin ranged from 33.2 to 62.5 ng/mL across all 4 weeks. The addition of wheat crackers to the adult human subjects' usual diet had a minimal impact on their gastrointestinal inflammation or the gut microbiota. [ABSTRACT FROM AUTHOR]

Summary: Oral tolerance promotes the suppression of immune responses to innocuous antigen and is primarily mediated by regulatory T cell (Tregs). The development of oral tolerance begins in early life during a "window of tolerance," which occurs around weaning and is mediated by components in breastmilk. Herein, we review the factors dictating this window and how Tregs are uniquely educated in early life. In early life, the translocation of luminal antigen for Treg induction is primarily dictated by goblet cell‐associated antigen passages (GAPs). GAPs in the colon are negatively regulated by maternally‐derived epidermal growth factor and the microbiota, restricting GAP formation to the "periweaning" period (postnatal day 11–21 in mice, 4–6 months in humans). The induction of solid food also promotes the diversification of the bacteria such that bacterially‐derived metabolites known to promote Tregs—short‐chain fatty acids, tryptophan metabolites, and bile acids—peak during the periweaning phase. Further, breastmilk immunoglobulins—IgA and IgG—regulate both microbial diversity and the interaction of microbes with the epithelium, further controlling which antigens are presented to T cells. Overall, these elements work in conjunction to induce a long‐lived population of Tregs, around weaning, that are crucial for maintaining homeostasis in adults. [ABSTRACT FROM AUTHOR]

Studies have shown that the microbiome of saline‐tolerant plants plays a significant role in promoting salt stress in non‐saline‐tolerant plants, but the microorganisms are still unclear. In the present study, the microbial diversity changes in Suaeda salsa (L.) Pall. in the Yellow River Delta region were investigated. In the bacterial community, the dominant bacteria in the rhizosphere soil of the low‐saline soil (YDL), moderate‐saline soil (YDM), and high‐saline soil (YDH) groups were Proteobacteria, Chloroflexi, Bacteroidota, and Actinobacteriota (at the phylum level), while Ascomycota and Basidiomycota were the dominant fungi in the fungal community. At the family level, with the increase of salinity, the relative abundance of Rhodobacteraceae (bacterial community), Thermoascaceae, and Phaffomycetaceae (fungal community) gradually increased; and to the best of our knowledge, there are no reports on the relationship between Thermoascaceae and Phaffomycetaceae families with salt stress. At the genus level, Salinimicrobium (bacterial community) was the dominant bacterium in the rhizosphere soil of the YDL, YDM, and YDH groups, while with the increase of salinity, the relative abundance of Byssochlamys and Wickerhamomyces (fungal community) gradually increased, and to the best of our knowledge there are no reports on the relationship between Byssochlamys and salt stress. Salinity mainly affected the bacterial community abundance, but it had little effect on the fungi community abundance. The bacterial community of the YDH group was dominated by bacteria of unknown origin (52.76%), while bacteria of unknown origin accounted for 26.46% and 20.78% of the bacterial communities in the YDM and YDL groups, respectively. The fungi community of the YDH group was dominated by YDL group fungi (relative abundance of 44.44%), followed by YDM group fungi (29.42%) and fungi of unknown origin (26.14%). These results provide a better understanding of the rhizosphere microbial diversity of saline–alkali‐tolerant plants, laying a foundation for developing a saline–alkali‐tolerant plant microbiome. Studies have shown that the microbiome of saline‐tolerant plants plays a significant role in promoting salt stress in non‐saline‐tolerant plants, but the microorganisms and their mechanisms are still unclear. In this study, the Suaeda salsa (L.) Pall. in Yellow River Delta region was selected to study the changes of microbial diversity. These results can provide valuable information for understanding the rhizosphere microbial diversity of saline–alkali‐tolerant plants, and lay a foundation for developing saline–alkali‐tolerant plant microbiome. [ABSTRACT FROM AUTHOR]

Although bold and shy behavioral phenotypes in zebrafish (Danio rerio) have been selectively bred and maintained over multiple generations, it is unclear if they are underscored by different gut microbiota. Using the microbiota–gut–brain concept, we examined the relationship between gut microbiota and the behavioral phenotypes within this model animal system to assess possible gut microbe‐mediated effects on host behavior. To this end, we amplified and sequenced 16S rRNA gene amplicons from the guts of bold and shy zebrafish individuals using the Illumina Miseq platform. We did not record any significant differences in within‐group microbial diversity nor between‐group community composition of the two behavioral phenotypes. Interestingly, though not statistically different, we determined that the gut microbial community of the bold phenotype was dominated by Burkholderiaceae, Micropepsaceae, and Propionibacteriaceae. In contrast, the shy phenotype was dominated by Beijerinckaceae, Pirelullacaeae, Rhizobiales_Incertis_Sedis, and Rubinishaeraceae. The absence of any significant difference in gut microbiome profiles between the two phenotypes would suggest that in this species, there might exist a stable core gut microbiome, regardless of behavioral phenotypes, and possibly, a limited role for the gut microbiota in modulating this selected‐for host behavior. This study characterized the gut microbiomes of distinct innate behavioral phenotypes of the zebrafish (that are not considered dysbiotic states) and did not rely on antibiotic or probiotic treatments to induce changes in behavior. Such studies are crucial to our understanding of the modulating impacts of the gut microbiome on normative animal behavior. [ABSTRACT FROM AUTHOR]

Soil microbial diversity is a vital factor for the progression of vegetation and biogeochemical cycles in an ecosystem. It is affected by the chemical composition, soil microenvironment and anthropogenic activities. The present study investigated the effect of environmental conditions and anthropogenic activities on the bacterial diversity of three distantly related soils in India. The multiple soil samples were collected from Hospital waste sites (BTC2) with extensive anthropogenic activity, Himalayan forest soil (RM1) with low anthropogenic activity and Tso Kar Lake sediment soil samples with negligible anthropogenic activity with environmental factors such as soil pH, temperature and altitude on the bacterial diversity. The soil samples were analyzed for physico-chemical properties that suggest significant variations in pH, electrical conductivity (EC), total dissolved solids (TDS), temperature and altitude. The SEM-EDS (Scanning electron microscopy with energy-dispersive X-ray spectroscopy) analysis revealed the elemental composition of the soil samples. The bacterial diversity of three different soil samples was studied using 16S rRNA sequencing-based metagenomic analysis. The results suggested that the bacterial diversity in Hospital waste site soil samples was higher than in the other two soil samples based on chao1 (richness and evenness) analysis. The Phyla Firmicutes were more abundant in Hospital waste site soil, and Himalayan forest soil showed a higher abundance of phylum Proteobacteria (28.86%) and Actinobacteria (26.70%). Tso Kar Lake sediment soil samples showed the most abundant phylum as Proteobacteria (46.28%). The study suggests that increased anthropogenic activity increases soil bacterial diversity. It may eventually help to develop new approaches for sustainable land-use management practices. [ABSTRACT FROM AUTHOR]

Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research. [ABSTRACT FROM AUTHOR]

Gelsemium elegans Benth. (Loganiaceae), also known as heartbreak herb, can be used in the manufacture of herbal medicines. Insecticidal activity has also been found and can be used to develop botanical insecticides. This study aimed to reveal the insecticidal mechanism of its extracts against red fire ants and provide strategies for the development of biopesticides and the promotion of green and sustainable agriculture. 16s rRNA, pathohistological, behavioral, and enzyme activity assays were performed to reveal its biological effects, including the effects on non-target organisms. Our results showed that red fire ants exposed to G. elegans extracts exhibited slowed growth, reduced feeding, and decreased aggressiveness. The midgut and its peritrophic membrane of red fire ant were significantly disrupted, the diversity of gut microbial community was reduced, and the balance of microbial composition was disturbed. Significant increases in functional abundance of xenobiotics biodegradation and metabolism pathway and P450s enzyme activity confirmed the toxic stress of G. elegans extract. Functional prediction of Kyoto Encyclopedia of Genes and Genomes pathway showed that the functional abundance of novobiocin biosynthesis, flavonoid biosynthesis, lysosome, proteasome, and wingless/integrated signaling pathways were significantly inhibited in the gut. Besides, G. elegans extracts induced an increase in acetylcholinesterase activity. These results revealed dysregulation of immune system and metabolic functions in red fire ants, as well as toxic effects of G. elegans extracts on physiological functions and nerves. These findings revealed the insecticidal mechanism of G. elegans and supported the development of eco-friendly insecticides for red fire ants. [ABSTRACT FROM AUTHOR]

The gut microbiota plays an essential role in maintaining immune homeostasis and influencing the immune landscape within the tumor microenvironment. This review aims to elucidate the interactions between gut microbiota and tumor immune dynamics, with a focus on colorectal cancer (CRC). The review spans foundational concepts of immuno-microbial interplay, factors influencing microbiome composition, and evidence linking gut microbiota to cancer immunotherapy outcomes. Gut microbiota modulates anti-cancer immunity through several mechanisms, including enhancement of immune surveillance and modulation of inflammatory responses. Specific microbial species and their metabolic byproducts can significantly influence the efficacy of cancer immunotherapies. Furthermore, microbial diversity within the gut microbiota correlates with clinical outcomes in CRC, suggesting potential as a valuable biomarker for predicting response to immunotherapy. Conclusions: Understanding the relationship between gut microbiota and tumor immune responses offers potential for novel therapeutic strategies and biomarker development. The gut microbiota not only influences the natural history and treatment response of CRC but also serves as a critical modulator of immune homeostasis and anti-cancer activity. Further exploration into the microbiome's role could enhance the effectiveness of existing treatments and guide the development of new therapeutic modalities. [ABSTRACT FROM AUTHOR]

Simple Summary: This study was the first attempt to use heat-killed Lactobacillus acidophilus as a feed additive to replace antibiotics. The results of the evaluation showed that it could improve the performance of piglets, increase intestinal microbial diversity and thus ensure the intestinal health of piglets. In conclusion, this provides a reference for the application of heat-killed Lactobacillus acidophilus. Probiotics can improve animal growth performance and intestinal health. However, understanding the effects of paraprobiotics on the growth performance and gut microbiota of piglets and how the paraprobiotics exert their impact are still limited. The present study was conducted to investigate the effects of heat-killed Lactobacillus acidophilus IFFI 6005 supplementation on the growth performance, intestinal microbiota, and fecal metabolites of piglets. First, a feed-additive sample of heat-killed Lactobacillus acidophilus IFFI 6005 was prepared by culture. Second, 96 (initial BW = 14.38 ± 0.67 kg, weaning age of 40 days) healthy piglets were selected and randomized into four treatment groups. Each treatment group consisted of three replicates (n = 8). Pigs were fed a basal diet (NC), basal diet plus antibiotics (PC), basal diet plus Lactobacillus acidophilus IFFI 6005 at 600 g/t (LA, 1.0 × 1010 cfu/g), and basal diet plus heat-killed Lactobacillus acidophilus IFFI 6005 at 600 g/t (HKLA), respectively; the trial lasted for 30 days. The results showed that the ratios of feed to gain (F:G) and diarrhea rate of both the HKLA and PC groups were significantly lower compared with the NC and LA groups (p < 0.05); however, there was no significant difference between the HKLA and PC group (p > 0.05). In addition, the average daily weight gain (ADG) of the HKLA group was significantly higher (p < 0.05) than that of the other three groups in terms of growth performance. Finally, 16S rRNA sequencing and metabolome analysis based on fecal samples further elaborated that the addition of heat-killed Lactobacillus acidophilus IFFI 6005 to the feed improved the intestinal microbial diversity and abundance (p < 0.05) and reduced the abundance of pathogenic bacteria (p < 0.05), but it did not affect the abundance of Lactobacillus (p > 0.05). Through the comparison of microbial abundance and metabolite content between the two groups (NC_vs_HKLA), the largest differences were found in six microorganisms and 10 metabolites in the intestine (p < 0.05). These differential metabolites were involved in the digestion, absorption and utilization of protein and starch, as well as in oxidative stress. In summary, addition of heat-killed Lactobacillus acidophilus IFFI 6005 as a new feed additive in piglets has beneficial effects on the growth performance, intestinal bacteria and metabolites, and can be used as an alternative to antibiotics. [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 "limón sutil" (Citrus aurantifolia) has been widely cultivated and well established for many years in Piura, northwestern Peru, because of its exceptional climate and soil conditions. However, decline and death of C. aurantifolia trees caused by different phytopathogens remain a common problem which has been observed in the last decades. It is known that the microbiota of soil plays an important role with their host and could be the starting point to understand the causes of citrus decline. In this study, we identified through culture-independent methods the bacterial and fungal microbiota associated to C. aurantifolia, C. jambhiri and C. volkameriana rhizospheres in the main areas of Piura. By using a 16S rRNA and ITS-metabarcoding analysis, we evaluated the taxonomic diversity between healthy trees and with decline symptoms and how this diversity could influence the health status of citrus trees. More than 600 and 200 bacterial and fungal ASVs were identified, respectively. Our metabarcoding analysis was able to identify Proteobacteria, Cyanobacteria, Firmicutes, Bacteroidota and Acidobacteriota prokaryotic phyla, while fungal phyla included Ascomycota, Basidiomycota and Glomeromycota. In addition, there were differences between microbial diversity indices in rhizospheres evaluated. Finally, bacterial and fungal genera were shared among the different citrus rhizospheres. These results have allowed us to obtain a preliminary identification of microbiota in the citrus rhizospheres of healthy trees and with decline symptoms. [ABSTRACT FROM AUTHOR]

Mangroves are one of the world's most unique tropical coastal ecosystems. They are a rich repository of biological wealth, including specially adapted flora and fauna. The microbiome component of this ecosystem is a fascinating world that is yet to be fully explored for its functional and ecological interrelationships with its hosts. The mangrove ecosystem is a hidden treasure of microbial diversity, without which mangrove biology is incomplete. In the present study, the isolation of a cellulase-producing, endophytic Bacillus sp. from the hypocotyl region of viviparous seedlings is described. This study urges us to look into the microbial diversity of mangrove propagules, by presenting a glimpse of a member of the endospheric microbiome of viviparous hypocotyls. [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]