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The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the composition and function of microbial communities, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations. A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive/athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed. Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. Most of studies reported an increase in short-chain fatty acid-producing bacteria such as Akkermansia , Faecalibacterium , Veillonella or Roseburia in active individuals and after physical activity interventions. Physical activity levels were positively associated with the relative abundance of short-chain fatty acid-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids obtaining conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome. [ABSTRACT FROM AUTHOR]

Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae , enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates. [Display omitted] • Antibiotics and non-antibiotic drugs govern infant gut microbiome development • Antibiotic-associated microbial shifts introduce pathogens and resistance • Hospitalized preterm infants share isogenic C. difficile and S. epidermidis • Microbial development stagnates before late-onset necrotizing enterocolitis Preterm neonates undergo numerous interventions. Thänert, Schwartz, Keen, et al. use multi-omics to show that antibiotics and other drugs alter gut microbiome development, but prenatal factors do not. Microbiome development stagnates before necrotizing enterocolitis ensues, but only among infants who experience this devastating complication after 40 days of life. [ABSTRACT FROM AUTHOR]

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Secondary metabolites made by plants and used through their metabolic routes are today's most reliable and cost-effective way to make pharmaceuticals and improve health. The concept of genetic engineering is used for molecular pharming. As more people use plants as sources of nanotechnology systems, they are adding to this. These systems are made up of viruses-like particles (VLPs) and virus nanoparticles (VNPs). Due to their superior ability to be used as plant virus expression vectors, plant viruses are becoming more popular in pharmaceuticals. This has opened the door for them to be used in research, such as the production of medicinal peptides, antibodies, and other heterologous protein complexes. This is because biotechnological approaches have been linked with new bioinformatics tools. Because of the rise of high-throughput sequencing (HTS) and next-generation sequencing (NGS) techniques, it has become easier to use metagenomic studies to look for plant virus genomes that could be used in pharmaceutical research. A look at how bioinformatics can be used in pharmaceutical research is also covered in this article. It also talks about plant viruses and how new biotechnological tools and procedures have made progress in the field. [ABSTRACT FROM AUTHOR]

INTRODUCTION: Emerging evidence links changes in the gut microbiome to late‐onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome. METHODS: We used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock‐in (hAβ‐KI) murine model for LOAD compared to both wild‐type (WT) mice and a model for early‐onset AD (3xTg‐AD). RESULTS: Eighteen‐month female (but not male) hAβ‐KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ‐KI mice microbiomes were distinguishable from 3xTg‐AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups. DISCUSSION: These findings highlight a sex‐dependent variation in the microbiomes of hAβ‐KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD. Highlights: Microbial diversity and the abundance of several species differed in human amyloid beta knock‐in (hAβ‐KI) females but not males.Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome.Microbiomes from hAβ‐KI mice were distinct from 3xTg‐AD mice.Cage effects accounted for most of the variance in the microbiome and metabolome. [ABSTRACT FROM AUTHOR]

This retrospective study was conducted to investigate the application value of metagenomics next generation sequencing (mNGS) technology in the diagnosis and treatment of neonatal infectious meningitis. From 1 January 2020 to 31 December 2022, 73 newborns suspected of infectious meningitis were hospitalized. After screening by inclusion and exclusion criteria, 69 newborns were subsequently included in the study, containing 27 cases with positive mNGS result and 42 cases with negative mNGS result. Furthermore, according to the diagnosis of meningitis, mNGS positive group and mNGS negative group were further divided into infectious meningitis with mNGS (+) group (n = 27) and infectious meningitis with mNGS (-) group (n = 26), respectively. (1) Compared with cerebrospinal fluid (CSF) culture, mNGS has better diagnostic value [positive predictive value (PPV) = 100.00% (27/27), negative predictive value (NPV) = 38.10% (16/42), agreement rate = 62.32% (43/69), area under the curve (AUC) = 0.750, 95% confidence interval (CI): 0.636–0.864]. (2) There were significant differences in the onset age, age at first CSF test, CSF leukocyte count, CSF glucose, positive rate of CSF culture, blood leukocyte count, procalcitonin (PCT), C-reaction protein (CRP), age at first mNGS test and adjusting anti-infective medication in the comparison between infectious meningitis with mNGS (+) group and infectious meningitis with mNGS (-) group (p < 0.05). (3) mNGS could help improve the cure rate [crude odds ratio (OR) = 3.393, 95%CI: 1.072–10.737; adjusted OR = 15.580, 95%CI: 2.114–114.798]. Compared with classic meningitis detection methods, mNGS has better PPV, NPV, agreement rate, and AUC. mNGS could help improve the cure rate. [ABSTRACT FROM AUTHOR]

Rapid growth in aquaculture has resulted in high-density production systems in ecologically and geographically novel conditions in which the emergence of diseases is inevitable. Well-characterized methods for detection and surveillance of infectious diseases are vital for rapid identification, response, and recovery to protect economic and food security. We implemented a proof-of-concept approach for virus detection using a known high-consequence fish pathogen, infectious salmon anemia virus (ISAV), as the archetypal pathogen. In fish infected with ISAV, we integrated histopathology, virus isolation, whole-genome sequencing (WGS), electron microscopy (EM), in situ hybridization (ISH), and reverse transcription real-time PCR (RT-rtPCR). Fresh-frozen and formalin-fixed tissues were collected from virus-infected, control, and sham-infected Atlantic salmon (Salmo salar). Microscopic differences were not evident between uninfected and infected fish. Viral cytopathic effect was observed in cell cultures inoculated with fresh-frozen tissue homogenates from 3 of 3 ISAV-infected and 0 of 4 uninfected or sham-infected fish. The ISAV genome was detected by shotgun metagenomics in RNA extracted from the medium from 3 of 3 inoculated cell cultures, 3 of 3 infected fish, and 0 of 4 uninfected or sham-infected fish, yielding sufficient coverage for de novo assembly. An ISH probe against ISAV revealed ISAV genome in multiple organs, with abundance in renal hematopoietic tissue. Virus was detected by RT-rtPCR in gill, heart, kidney, liver, and spleen. EM and metagenomic WGS from tissues were challenging and unsuccessful. Our proof-of-concept methodology has promise for detection and characterization of unknown aquatic pathogens and also highlights some associated methodology challenges that require additional investigation. [ABSTRACT FROM AUTHOR]

Personalised medicine is a rapidly evolving field to which many resources have been devoted recently. It represents a paradigm shift from a one-size-fits-all approach to healthcare, focusing instead on tailoring treatments and diagnoses to individual patients. This study aims to contribute to this transition by leveraging recent advancements in microbiome research. An earlier study that computed the Gut Microbiome Health Index (GMHI), a potent indicator capable of predicting disease presence with approximately 70% of accuracy, serves as the foundation for this research. Positive values of the GMHI are associated with healthy subjects and negative values to non-healthy ones. The objective of this study is twofold: firstly, to advance the use of the GMHI through the application of two distinct machine learning techniques, a Fully Connected Neural Network and an Autoencoder, secondly, to adapt the GMHI for a unique dataset of COVID-19 patients. The employment of these two neural network architectures facilitated an enhancement in predictive accuracy to approximately 74.5%, surpassing the GMHI baseline accuracy of 70.95%. Simultaneously, the application of the GMHI, recalibrated using species specifically identified in the COVID-19 dataset, demonstrated a substantial increase in accuracy by 17% (achieving an accuracy of 76%). These promising results in distinguishing COVID-19 patients, highlight the potential and broad applicability of this approach in the sphere of personalized medicine and directly relating the COVID-19 disease to one's microbiome and its composition. [ABSTRACT FROM AUTHOR]

The fungal communities of mangrove sediments have wide ecological significance and are actively involved in nutrient recycling, decomposition of litter and degradation of recalcitrant substances. The present study focused on comparing the abundance, diversity and composition of fungal community in the sediments of two selected mangrove ecosystems of Kannur and Eranakulam districts of Kerala. Metagenomic analysis of the total sediment DNA was performed on an Illumina sequencing platform using fungal ITS primers. The number of Operational Taxonomic Units (OTUs) and the diversity indices showed that the Eranakulam mangrove sediments possessed higher fungal abundance, species richness and diversity than the mangrove sediments of Kannur. Ascomycota was most predominant phyla identified and a total of 11 classes, 20 orders, 34 families and 36 genera were obtained from the mangrove sediments. Talaromyces, which is not a commonly reported genus from Indian mangroves was the most prominent genera found in our study. The diversity heat map showed that 16 genera were exclusive to Eranakulam mangrove sediments while 5 genera were exclusive to Kannur samples. The metagenomics data of the mangrove sediments in our study revealed the presence of many fungal strains with vast biotechnological potential which can be further explored in the technology development. [ABSTRACT FROM AUTHOR]

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics. Highlights: Soil carries diverse microorganisms which maintain plant and soil health. The different types of recalcitrant soil pollutants affect the ecosystem and human health. Complex pollutants can be degraded through bioremediation using microorganisms/plants Metagenomic approaches help to explore novel organisms and enzymes involved in bioremediation. [ABSTRACT FROM AUTHOR]

Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events. [ABSTRACT FROM AUTHOR]

Background: Because little is known about the impact of implant surface modifications on the peri‐implant microbiome, we aimed to examine peri‐implant communities in various surface types in order to better understand the impact of these surfaces on the development of peri‐implantitis (PI). Methods: One hundred and six systemically healthy individuals with anodized (AN), hydroxyapatite‐coated (HA), or sandblasted acid‐etched (SLA) implants that were >6 months in function were recruited and categorized into health (H) or PI. Peri‐implant biofilm was analyzed using 16S rRNA gene sequencing and compared between health/disease and HA/SLA/AN using community‐level and taxa‐level metrics. Results: Healthy implants did not demonstrate significant differences in clustering, alpha‐ or beta‐diversity based on surface modification. AN and HA surfaces displayed significant differences between health and PI (p < 0.05); however, such a clustering was not evident with SLA (p > 0.05). AN and HA surfaces also differed in the magnitude and diversity of differences between health and PI. Six species belonging to the genera Shuttleworthia, Scardovia, and Prevotella demonstrated lower abundances in AN implants with PI, and 18 species belonging to the genera Fretibacterium, Tannerella, Treponema, and Fusobacterium were elevated, while in HA implants with PI, 20 species belonging to the genera Streptococcus, Lactobacillus, Veillonella, Rothia, and family Ruminococcaceae were depleted and Peptostreptococcaceae, Atopobiaceae, Veillonellaceae, Porphyromonadaceae, Desulfobulbaceae, and order Synergistales were enriched. Conclusions: Within the limitations of this study, we demonstrate that implant surface can differentially modify the disease‐associated microbiome, suggesting that surface topography must be considered in the multi‐factorial etiology of peri‐implant diseases. [ABSTRACT FROM AUTHOR]

Bovine hepacivirus (BoHV) is closely related to the hepatitis C virus (HCV) in humans and can cause both acute and chronic liver infections in cattle. BoHV was first identified in Ghana and Germany in 2015 and since then it has been detected and characterized in other countries around the world, but no strains have been sequenced from U.S. cattle. To date, BoHV has been classified into 2 genotypes (1 and 2), with genotype 1 being further divided into 11 subtypes (A–K). However, the true genetic diversity of BoHV is likely underestimated given limited surveillance and a lack of published genome sequences. Here, we sequenced 2 nearly complete BoHV genomes from serum samples collected in 2019 from beef cattle in Missouri. Sequence comparisons and phylogenetic analysis showed that isolate MARC/2019/60 had high sequence homology with genotype 1, subtype E isolates from China. In contrast, isolate MARC/2019/50 represented a novel BoHV subtype within genotype 2. Thus, we report the first genomic characterization of BoHV isolates from U.S. cattle, and the second complete BoHV2 genome worldwide. This work increases our knowledge of the global genetic diversity of BoHV and demonstrates the co-circulation of divergent BoHV strains in U.S. cattle. [ABSTRACT FROM AUTHOR]

Infections of the central nervous system (CNS) are potentially life-threatening and can cause serious morbidity. We evaluated the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of infectious encephalitis and meningitis and explored the factors affecting the results of mNGS. Patients with suspected cases of encephalitis or meningitis who presented in Northern Jiangsu People's Hospital from 1 March 2018 to 30 September 2022 were collected. Demographic, historical, and clinical information were obtained, and cerebrospinal fluid (CSF) samples were treated with mNGS. The pathogen was identified using National Center for Biotechnology Information (NCBI) GenBank sequence data. Ninety-six patients were screened and finally 90 subjects enrolled. Of the 90 enrolled cases, 67 (74.4%) were diagnosed with central nervous system infections, which included 48 cases (71.6%) of viral infection, 11 (12.2%) of bacterial infection, 5 (7.5%) of mycobacterium tuberculosis, 2 (3.0%) of fungal infection, and 1 (1.5%) of rickettsia infection. From these cases, mNGS identified 40 (44.4%) true-positive cases, 3 (3.3%) false-positive case, 22 (24.4%) true-negative cases, and 25 (27.8%) false-negative cases. The sensitivity and specificity of mNGS were 61.5% and 88%, respectively. mNGS of CSF could show a higher positive rate in patients with marked CSF abnormalities, including elevated protein concentrations and monocyte counts. mNGS of CSF is an effective method for detecting infectious encephalitis and meningitis, and the results should be analyzed combined with conventional microbiological testing results. [ABSTRACT FROM AUTHOR]

Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads. However, the cultivation of only about 1% of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria. Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods. This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening, sequence tag-based homology screening, and bioinformatic-assisted chemical synthesis. Through this process, numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories. This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries. [ABSTRACT FROM AUTHOR]

Pathogen agnostic sequencing, also known as metagenomic sequencing, is a useful tool for biodefense and public health surveillance. It involves sequencing genetic material in a sample to detect and monitor infectious diseases. Next-generation sequencing technologies have made this method more affordable and accessible. The US Department of Defense's Global Emerging Infections Surveillance program has successfully integrated pathogen agnostic sequencing into its infectious disease surveillance network. The program has established a consortium to promote collaboration and standardization, conducted proficiency testing exercises, and funded surveillance activities using this method. The text discusses the challenges and opportunities associated with pathogen agnostic sequencing, highlighting the need for standardized protocols and methods, as well as collaboration between the biodefense and public health communities. The conclusion emphasizes the value of past investments in this technology and the need for continued investment to prepare for future threats. [Extracted from the article]

Saliva, an oral secretion is considered an essential biological modulator involved in maintaining oral homeostasis. Increased glucose levels in diabetic patients' saliva may have an impact on diversity of microbes. Comparing the salivary microflora of diabetic and non-diabetic cohorts will help in diagnosis and risk assessment of oral health complications. This will provide greater knowledge about the contribution of oral microbes to the development of oral illnesses. The association between salivary microbiota and diabetic state is less explored in the North Indian population, hence current observational study was performed to analyze the salivary microflora of diabetic and non-diabetic individuals using metagenomic analysis. This single-center non-randomized observational trial was conducted in Uttar Pradesh, India. Participants were enrolled into either diabetic (n = 68) or non-diabetic groups (n = 68) based on their diabetes status. Following saliva collection, DNA was extracted and metagenomic sequencing was performed. Phylum Bacteroidetes and Fusobacteria were significantly abundant in diabetic individuals (p < 0.0001), while Proteobacteria was significantly higher among non-diabetic individuals (p < 0.0001). No statistical difference in phylum Actinobacteria and Firmicutes among diabetics and non-diabetics. Veillonella, Prevotella, Porphyromonas, Leptotrichia, Lactobacillus, and Streptococcus were greater in diabetics whereas the abundance of Capnocytophaga and Neisseria was more among non-diabetics (p < 0.05). The genera Veillonella, Prevotella, Porphyromonas, Leptotrichia, Lactobacillus, and Streptococcus were comparatively over the odds with the diabetics in India. The association between microbiota in diabetic population and risk related to increase in occurrence of caries, gingivitis, and periodontitis in diabetic population prevalence should be investigated. [ABSTRACT FROM AUTHOR]

This study aimed to comprehend the diversity of the fungal community on Chokanan mango, a premium mango variety from Thailand which is widely cultivated in Indonesia, associated with stem end rot and anthracnose disease using high-throughput amplicon targeted metagenomics analysis by next-generation sequencing (NGS). Samples used in this study were freshly harvested healthy fruits at the age of 15-weeks (H15.ITS), healthy fruits after 2 weeks incubation (H17.ITS), 17-week old fruits (S17.ITS) with stem end rot symptoms, and 17-week old fruits (A17.ITS) with anthracnose symptoms. Results showed that the Basidiomycota phylum was dominant in the healthy fruits, while the Ascomycota phylum was found dominantly in sick fruits. Based on OTUs alignment of sequenced data, some species found to be dominantly associated with stem end rot disease in this study were Lasiodiplodia theobromae, Neofusicoccum cordaticola and N. mangiferae. Dominant species which were associated with mango anthracnose disease were Colletotrichum gloeosporioides, Botryosphaeria corticis, Volutella sp., and Pseudofusicoccum violacearum. These fungal genera were not found to be dominant in healthy fruits at the same age indicating that specific genera contributed to developing postharvest diseases on mango differently. The findings confirmed that the fungal community associated with stem end rot and anthracnose disease on mango was unique, and specific species contributed in particular disease development. Since mango is an important global commodity, these research findings will contribute significantly to global biosecurity. [ABSTRACT FROM AUTHOR]

This article discusses the role of microbial rhodopsins in capturing solar energy in the ocean. While most photosynthetic organisms use chlorophyll to convert sunlight into energy, microbial rhodopsins use the pigment retinal. These proteins are found in both eukaryotes and prokaryotes, including bacteria and viruses. The discovery of microbial rhodopsins has expanded our understanding of energy capture and productivity in marine ecosystems. They are particularly abundant in low-nutrient environments and provide enough energy to sustain basal metabolism and promote survival. Additionally, microbial rhodopsins have potential applications in optogenetics and the engineering of non-phototrophic organisms to harvest energy from light. [Extracted from the article]

The mechanisms modulated by periodontal pathogens in atherosclerosis are not fully understood. Aim: to perform an integrative analysis of gene and protein expression modulated by periodontal pathogens in cells and animal models for atherosclerosis. Cochrane, PRISMA and AMSTAR2 guidelines for systematic reviews were followed. Data search was conducted in Pub-med, LILACS and Science Direct databases. Gene and protein expression data were collected from the included papers to perform an overrepresentation analysis using the Reactome Pathway Analysis tool and the KEGG database. Thirty-two papers were included in the review, they analyzed the effect of Fusobacterium nucleatum , Porphyromonas gingivalis , Streptococcus anginosus , Streptococcus sanguinis , Tannerella forsythia , and Treponema denticola or/and their virulent factors on gene and protein expression in human cells and animal models of atherosclerosis. Some of the modulated pathways include the immune system, programmed cell death, cellular responses to external stimuli, transport of small molecules, and signal transduction (p < 0.05). Those pathways are known to be involved in different stages of atherosclerosis progression. Based on the performed analysis, it is possible to state that periodontal pathogens have the potential to be a contributing factor for atherosclerosis even in absence of a high-fat diet or high shear stress. [ABSTRACT FROM AUTHOR]

Background The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge. Results To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances. Conclusion Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section. [ABSTRACT FROM AUTHOR]

Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA. In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae , we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture. Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p < 0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing. Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future. [Display omitted] [ABSTRACT FROM AUTHOR]

To evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of central nervous system infections (CNSI). Cerebrospinal fluid (CSF) from 54 patients who were high-level clinical suspicion of CNSI was collected and sent for mNGS and conventional tests from January 2019 to March 2022. Twenty out of 54 patients were diagnosed with CNSI and 34 non-CNSI. Among the 34 non-CNSI, one was false positive by mNGS. Among the 20 CNSI, 11 had presumed viral encephalitis and/or meningitis, 5 had presumed bacterial meningitis, 2 had presumed TMB, 1 had Crytococcus meningitis and 1 had neurosyphilis. The sensitivity of viral encephalitis and/or meningitis was 0.73 (8/11); 10 virus were detected; 9/10 was dsDNA; 1/10 was ssRNA. SSRN ranged from 1 to 13. The accuracy rate was 0.4, the accuracy rate was positively correlated with SSRN (r = 0.738, P = 0.015), SSRN ≥ 1, the accuracy rate was 0.4; SSRN ≥ 3, the accuracy rate was 0.66; SSRN ≥ 4, the accuracy rate was 0.75; SSRN ≥ 6, the accuracy rate was 1. The sensitivity of bacterial meningitis was 1. Seven kinds of bacteria were detected, among which 3/7 were gram positive, 3/7 were gram negative, and 1/7 was infected NTM (nontuberculous mycobacteria). The accuracy rate was 0.43 (3/7). The sensitivity of TBM was 0.66 (2/3), the accuracy rate was 1. The sensitivity of Crytococcus meningitis was 1, the accuracy rate was 0.5. PPV (positive predictive value) of mNGS was 0.94, NPV (negative predictive value) of mNGS was 0.89, specificity was 0.97 and sensitivity was 0.8. The AUG for CSF mNGS diagnosis of CNSI was 0.89 (95% CI = 0.78–0.99) Headache, meningeal irritation sign and image of meninges abnormal were correlated with the sensitivity of mNGS (r = 0.451, 0.313, 0.446; p = 0.001, 0.021, 0.001); CSF Glucose and CSF Chloride were negatively correlated with sensitivity of mNGS (r = -0.395, −0.462; p = 0.003, ＜ 0.001). mNGS is a detection means with high sensitivity, wide coverage and strong timeliness, which can help clinicians to identify the pathogen diagnosis quickly, conduct targeted anti-infection treatment early and reduce antibiotic abuse. The pathogen which causing low CSF Glucose, low CSF Chloride or meninges infections was more likely to be detected by mNGS. It may be related to growth and structural characteristics of the pathogen and blood–brain barrier damage. [ABSTRACT FROM AUTHOR]

Background Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial 'enterotypes' associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success. Methods Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into 'viral community types', respectively. Results Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success. Conclusions This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance. [ABSTRACT FROM AUTHOR]

We report here a transiently culturable oomycete pathogen isolated from a pyogranulomatous tail mass in a cat. The organism was morphologically and genetically distinct from Lagenidium and Pythium species. Following next-generation sequencing (NGS) and assembly of contigs, initial phylogenetic analysis using fragments of the cox1 mitochondrial gene identified this specimen as Paralagenidium sp. after nucleotide alignments with sequences obtained from the Barcode of Life Data System (BOLD). However, further analysis of a concatenation of 13 different mitochondrial genes showed that this organism is unique and different from all known oomycetes. A negative PCR result using primers targeting known oomycete pathogens may not be enough to rule out oomycosis in a suspected case. Additionally, the use of a single gene to classify oomycetes may produce misleading results. The advent of metagenomic sequencing and NGS provides a unique opportunity to further explore the diversity of oomycetes as plant and animal pathogens beyond the current capabilities of global barcoding projects that are based on partial genomic sequences. [ABSTRACT FROM AUTHOR]

Background Soil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metagenomic analysis of the soybean endosphere (all microbial communities found in plant leaves) to reveal signatures of microbes for health and disease. Results The dataset is based on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) release "microbial diversity in soybean". The quality control process rejected 21 of the evaluated sequences (0.03% of the total sequences). Dereplication determined that 68,994 sequences were artificial duplicate readings, and removed them from consideration. Ribosomal Ribonucleic acid (RNA) genes were present in 72,747 sequences that successfully passed quality control (QC). Finally, we found that hierarchical classification for taxonomic assignment was conducted using MG-RAST, and the considered dataset of the metagenome domain of bacteria (99.68%) dominated the other groups. In Eukaryotes (0.31%) and unclassified sequence 2 (0.00%) in the taxonomic classification of bacteria in the genus group, Streptomyces, Chryseobacterium, Ppaenibacillus, Bacillus, and Mitsuaria were found. We also found some biological pathways, such as CMP-KDO biosynthesis II (from D-arabinose 5-phosphate), tricarboxylic acid cycle (TCA) cycle (plant), citrate cycle (TCA cycle), fatty acid biosynthesis, and glyoxylate and dicarboxylate metabolism. Gene prediction uncovered 1,180 sequences, 15,172 of which included gene products, with the shortest sequence being 131 bases and maximum length 3829 base pairs. The gene list was additionally annotated using Integrated Microbial Genomes and Microbiomes. The annotation process yielded a total of 240 genes found in 177 bacterial strains. These gene products were found in the genome of strain 7598. Large volumes of data are generated using modern sequencing technology to sample all genes in all species present in a given complex sample. Conclusions These data revealed that it is a rich source of potential biomarkers for soybean plants. The results of this study will help us to understand the role of the endosphere microbiome in plant health and identify the microbial signatures of health and disease. The MG-RAST is a public resource for the automated phylogenetic and functional study of metagenomes. This is a powerful tool for investigating the diversity and function of microbial communities. [ABSTRACT FROM AUTHOR]

To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China. Ten smear samples were collected in March 2019 Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus. We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01–S09 and S10. In S01–S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01–S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B. This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds [ABSTRACT FROM AUTHOR]

Metagenomic next-generation sequencing (mNGS) has been widely used for the detection of pathogens causing infectious diseases. This study aimed to evaluate the potential ability of mNGS to detect pathogens causing oral and maxillofacial space infection (OMSI) and compare the results with those of the traditional diagnostic microbial culture method. We retrospectively reviewed the data of 218 patients diagnosed with OMSI who underwent microbial culture and mNGS at the Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, from July 2020 to January 2022. The positivity rate of mNGS (216 cases) was significantly higher than that of microbial culture (123 cases). The most frequently detected bacteria were different between these two detection methods. Streptococcus constellatus (16.05%, 35), Streptococcus anginosus (15.69%, 34) and Klebsiella pneumoniae (6.88%, 15) were the most commonly isolated bacteria by culture. However, Peptostreptococcus stomatis (61.47%, 134), Parvimonas micra (68.35%, 149) and Streptococcus constellatus (57.34%, 125) were the most commonly detected bacteria by mNGS. mNGS also has advantages in diagnosing viral infections. The optimal numbers of diagnostic reads were 1162 and 588 for the diagnosis of Streptococcus anginosus and Streptococcus constellatus infections, respectively. Read numbers were significantly correlated with C-reactive protein (CRP), procalcitonin (PCT), and blood glucose levels and neutrophil percentage (NEUT%). For pathogens causing OMSI, mNGS had a higher rate of microbial pathogen detection and remarkable advantages in identifying coinfections involving viruses and fungi. The read numbers for mNGS are important for diagnostic accuracy and disease severity evaluation. [ABSTRACT FROM AUTHOR]

Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg−1 intramuscular, 3 consecutive days) or cefquinome (2 mg.kg−1 intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections. [ABSTRACT FROM AUTHOR]

Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed. [ABSTRACT FROM AUTHOR]

The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults. We sought to investigate the association and predictive capacity of the gut microbiome for incident asthma and chronic obstructive pulmonary disease (COPD). Shallow metagenomic sequencing was performed for stool samples from a prospective, population-based cohort (FINRISK02; N = 7115 adults) with linked national administrative health register–derived classifications for incident asthma and COPD up to 15 years after baseline. Generalized linear models and Cox regressions were used to assess associations of microbial taxa and diversity with disease occurrence. Predictive models were constructed using machine learning with extreme gradient boosting. Models considered taxa abundances individually and in combination with other risk factors, including sex, age, body mass index, and smoking status. A total of 695 and 392 statistically significant associations were found between baseline taxonomic groups and incident asthma and COPD, respectively. Gradient boosting decision trees of baseline gut microbiome abundance predicted incident asthma and COPD in the validation data sets with mean area under the curves of 0.608 and 0.780, respectively. Cox analysis showed that the baseline gut microbiome achieved higher predictive performance than individual conventional risk factors, with C-indices of 0.623 for asthma and 0.817 for COPD. The integration of the gut microbiome and conventional risk factors further improved prediction capacities. The gut microbiome is a significant risk factor for incident asthma and incident COPD and is largely independent of conventional risk factors. [ABSTRACT FROM AUTHOR]

Copyright of Revista de la Academia Colombiana de Ciencias Exactas, Físicas y Naturales is the property of Academia Colombiana de Ciencias Exactas, Fisicas y Naturales and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Antimicrobial resistance is a global threat to human, animal, and environmental health. In pig production, antimicrobials and heavy metals such as zinc oxide are commonly used for treatment and prevention of disease. Nevertheless, the effects of antimicrobials and heavy metals on the porcine resistome composition and the factors influencing this resistance profile are not fully understood. Advances in technologies to determine the presence of antimicrobial resistance genes in diverse sample types have enabled a more complete understanding of the resistome and the factors which influence its composition. The aim of this review is to provide a greater understanding of the influence of antimicrobial and heavy metal usage on the development and transmission of antimicrobial resistance on pig farms. Furthermore, this review aims to identify additional factors that can affect the porcine resistome. Relevant literature that used high-throughput sequencing or quantitative PCR methods to examine links between antimicrobial resistance and antimicrobial and heavy metal use was identified using a systematic approach with PubMed (NCBI), Scopus (Elsevier), and Web of Science (Clarivate Analytics) databases. In total, 247 unique records were found and 28 publications were identified as eligible for inclusion in this review. Based on these, there is clear evidence that antimicrobial and heavy metal use are positively linked with antimicrobial resistance in pigs. Moreover, associations of genes conferring antimicrobial resistance with mobile genetic elements, the microbiome, and the virome were reported, which were further influenced by the host, the environment, or the treatment itself. [ABSTRACT FROM AUTHOR]

The taxonomic and functional composition of microbial communities from environmental, agricultural, and therapeutic settings is increasingly being studied using metagenomic methodologies in large-scale genomic applications. This has led to exponential growth in the field and has impacted on healthcare, pharmacology and biotechnology. However, with the current methodologies, it is sometimes difficult to obtain conclusive identification of an organism. In addition, the growth of the metagenomic field has led to the creation of large amounts of data held by different hosts, which characterize data differently and make analysis difficult. Therefore, correct data aggregation and classification improve and facilitate the discovery of repositories of interest. This paper tackles these issues by proposing a methodology for organism identification, data aggregation and content characterization, visualization and selection. We propose a three-step pipeline for organism identification that uses compression-based metrics, an aggregation mechanism for content characterization, and a web database catalogue for data exposition and visualization. [ABSTRACT FROM AUTHOR]

Type 1 recombinant enterovirus G (EV-G), which carries the papain-like cysteine protease (PLCP) gene of torovirus between its 2C/3A regions, and type 2 recombinant EV-G, which carries the torovirus PLCP gene with its flanking regions having non-EV-G sequences in place of the viral structural genes, have been detected in pig farms in several countries. In a previous study, we collected 222 fecal samples from 77 pig farms from 2104 to 2016 and detected one type 2 recombinant EV-G genome by metagenomics sequencing. In this study, we reanalyzed the metagenomic data and detected 11 type 2 recombinant EV-G genomes. In addition, we discovered new type 2 recombinant EV-G genomes of the two strains from two pig farms samples in 2018 and 2019. Thus, we identified the genomes of 13 novel type 2 recombinant EV-Gs isolated from several pig farms in Japan. Type 2 recombinant EV-G has previously been detected only in neonatal piglets. The present findings suggest that type 2 recombinant EV-G replicates in weaning piglets and sows. The detection of type 1 recombinant EV-Gs and type 2 recombinant EV-Gs at 3-year and 2-year intervals, respectively, from the same pig farm suggests that the viruses were persistently infecting or circulating in these farms. [ABSTRACT FROM AUTHOR]

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Natural kefir grains are rich in beneficial bacteria, and analysis of their microbial diversity is a necessary condition for developing and applying kefir grains. In this study, six commercially available natural kefir grains were used as raw materials to explore their microbial diversity by metagenomics. The results showed that there were 14794 genes in 6 kinds of natural kefir grains, and the number of unique genes of X1, X2, X3, X4, X5, X6 were 111, 11, 0, 1899, 552, 1, respectively. From the relative abundance table of boundary, phylum, class, order, family, genus and species, the microbial diversity at each level was analyzed.The two dominant genera at the genus level are Lactobacillus and Lactococcus, and the dominant species at the species level are Lactococcus lactis and Lactococcus kefiranofaciens, Lactococcus crispatus, and Lactococcus helveticus, etc. Species distribution and species diversity of each sample were analyzed by species heat map, principal component analysis and non-metric multidimensional calibration methods. The results showed that the microbial diversity of natural kefir grains from 6 different sources were different. The research can provide reference for the development and application of natural kefir grains in the field of dairy products. [ABSTRACT FROM AUTHOR]

Tris(2-chloroethyl) phosphate (TCEP) is of growing public concern worldwide because of its ubiquitous contamination, toxicity, and persistence. In this study, we investigated bacterial communities in aerobic enrichment cultures with TCEP and its two major transformation products bis(2-chloroethyl) phosphate (BCEP) and 2-chloroethanol (2-CE) as the sole carbon source. Burkholderiales and Rhizobiales were likely two main bacterial guilds involved in the hydrolysis of TCEP, while Rhizobiales and Sphingomonadales may play an important role in the hydrolysis of BCEP, given the increase of Rhizobiales and Sphingomonadales-related phosphoesterase genes when the carbon source was switched from TCEP to BCEP. All Burkholderiales, Rhizobiales, Sphingomonadales were probably efficient in 2-CE metabolism, because their dehydrogenase genes and dehalogenase genes increased after 2-CE enrichment. The different substrate preference of different bacterial guilds highlighted the importance to understand the diversity and collaboration among functional bacteria. Meanwhile, two TCEP-degrading strains affiliated with Xanthobacter and Ancylobacter were isolated. Xanthobacter sp. strain T2-1 was able to degrade both TCEP and BCEP following the pseudo-first-order kinetics with reaction rates of 1.66 h−1 for TCEP and 1.02 h−1 for BCEP, respectively. Ancylobacter sp. strain T3-4 could degrade TCEP following the pseudo-first-order kinetics with a reaction rate of 2.54 h−1, but is unable to degrade BCEP. Additionally, strains that were phylogenetically closely related were found to have different degradation capabilities toward TCEP and/or BCEP, indicating the importance to investigate functional genes such as phosphoesterase genes. [Display omitted] • Different bacteria played specific roles during different TCEP degradation steps. • Burkholderiales and Rhizobiales were two main degraders during TCEP hydrolysis. • Rhizobiales and Sphingomonadales were important during BCEP hydrolysis. • Phylogenetically similar Isolates showed strain-specific degradation capability. [ABSTRACT FROM AUTHOR]

Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ13C of dissolved inorganic carbon (δ13C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers. [Display omitted] • Petroleum-hydrocarbon-contaminated red clay aquifers host carbon-fixing microbes. • Petroleum-hydrocarbons may enhance proliferation of carbon-fixing microorganisms. • Petroleum-hydrocarbon-contaminated aquifers hold carbon sequestration potential. [ABSTRACT FROM AUTHOR]

The livestock industry has long been a hotspot environment for antibiotic resistance genes, with smallholder farming still holding a significant position in pig farming. However, the microbial antibiotic resistance and pathogen risks in pigs under the smallholder farming model remain unclear. We systematically analyzed the antibiotic resistance and microbial composition of pig feces from smallholder and large-scale farming models in Sichuan. The results indicated a lower abundance of antibiotic resistance genes (ARGs) and similar microbial composition in smallholder farming compared to large-scale farming. Beneficial bacteria were more abundant in small-scale farming, whereas large-scale farming exhibited more ARGs, virulence genes, and human pathogenic bacteria (HPBs), including ESBL Escherichia coli strains closely related to human strains, indicating higher zoonotic risk. The findings suggest that smallholder farming presents a relatively better microbial composition and resistance profile, highlighting its advantages over large-scale farming in terms of pig and human health. It is noteworthy that a considerable proportion of HPBs carrying ARGs still exist in the feces from smallholder farming, and given the openness of fecal handling, there remains a high risk of transmitting ARGs and pathogens to humans. [Display omitted] • Smallholder farms contain a large number of high-risk ARGs and HPBs. • Smallholder farms show lower ARGs and HPBs compared to largscale farms. • Antibiotic-resistant HPBs are enriched in largescale farming models. • Despite fewer HPBs, smallholder farms exhibit a greater diversity of HPBs with ARGs. • ESBL E. coli in largescale farms are closer to human isolates than smallholder. [ABSTRACT FROM AUTHOR]

The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance. [Display omitted] • High- throughput sequencing of 122 samples from cecum of 5 rodent species. • Gene catalog includes ∼22.8 M non-redundant genes: 21.3 % bacterial, 0.1 % archaea, 8.9 % viruses, 3.0 % fungi. • Bacillota and Bacteroidota are dominant phyla; significant variation in species composition observed. • Wild rodents showed higher Bacteroidota levels; significant differences in microbiota compared to lab mice. • 3703 antibiotic resistance genes (ARGs) across 392 unique types, and 130 ARGs correlated with mobile genetic elements. [ABSTRACT FROM AUTHOR]

Arsenic (As) and polycyclic aromatic hydrocarbons (PAHs) are highly toxic, carcinogenic and teratogenic, and are commonly found in soils of industrial sites such as coking plants. They exert environmental stresses on soil microorganisms, but their compounding effects have not been systematically studied. Exploring the effects of compound contamination on microbial communities, species and genes is important for revealing the ecological damage caused by compound contamination and offering scientific insights into soil remediation strategies. In this study, we selected soil samples from 0 to 100 cm depth of a coking site with As, PAHs and compound contamination. We investigated the compound effects of As and PAHs on microbial communities by combining high-throughput sequencing, metagenomic sequencing and genome assembly. Compared with single contamination, compound contamination reduced the microbial community diversity by 10.68%–12.07% and reduced the community richness by 8.39%–18.61%. The compound contamination decreased 32.41%–46.02% of microbial PAHs metabolic gene abundance, 11.36%–19.25% of cell membrane transport gene abundance and 12.62%–57.77% of cell motility gene abundance. Xanthobacteraceae , the biomarker for compound contaminated soils, harbors arsenic reduction genes and PAHs degradation pathways of naphthalene, benzo [a]pyrene, fluorene, anthracene, and phenanthrene. Its broad metabolic capabilities, encompassing sulfur metabolism and quorum sensing, facilitate the acquisition of energy and nutrients, thereby conferring ecological niche advantages in compound contaminated environments. This study underscores the significant impacts of As and PAHs on the composition and function of microbial communities, thereby enriching our understanding of their combined effects and providing insights for the remediation of compound contaminated sites. [Display omitted] • As And PAHs compound contamination simplifies soil microbial communities. • Compound contamination reduces the abundance of key functional genes in microbial communities. • Representative species Xanthobacteraceae possesses As and PAHs metabolism functions. [ABSTRACT FROM AUTHOR]

The rhizosphere, a critical interface involving soil, plant roots, and microorganisms, plays a vital role in the feedback processes between plants and soil, especially under phosphorus (P) limiting conditions typical of subtropical forests. This study used a chronosequence design to investigate first-fourth successive planting rotations of Chinese fir (Cunninghamia lanceolata) plantations in Fujian Province, China, with stands around 17 years old. We employed a modified P fractionation assay and metagenomic sequencing to explore P cycling in the rhizosphere across different plantation rotations. Rhizosphere labile P concentrations increased significantly in the fourth rotation, alongside a consistent upward trend in moderately labile P throughout successive plantings. Conversely, stable P and residual P concentrations declined during successive plantings, signaling a shift toward more accessible P forms. From metagenomic analyses, the proportion of P transport processes (transportation of phosphonate, phosphate, and inorganic phosphate) gradually increased. Notably, abundances were significantly higher in the rhizosphere soil of the fourth Chinese fir planting rotation of the K01126 gene (involved in phosphate ester mineralization), the phnD gene (associated with phosphonate transport), functional genes related to the solubilization of inorganic phosphate, such as pqqB , pqqC , pqqE , and ppa , and the phoB gene (linked to P-starvation response regulation). The results indicate that functional microbes of the rhizosphere, dominated by Proteobacteria and Acidobacteria , are instrumental in changing P cycling processes during successive plantings. The successive planting rotations of Chinese fir plantations significantly and positively impacted on the gene abundance related to the activation and uptake of P in the rhizosphere. Based on these insights, specific strategies, such as regular monitoring and application of phosphate fertilizer and adjusting rotation timing based on the soil rhizosphere P status, and incorporating native broad-leaved tree species are suggested to promote efficient P cycling, thus supporting sustainable forest management practices. [Display omitted] • Rhizosphere phosphorus and metagenomics probed in Chinese fir plantation rotations. • Increased rhizosphere soil labile P concentration with successive plantings. • Enhanced microbial genes for P activation and uptake with successive plantings. • Different rhizosphere soil P fractions correlated with key P cycling processes. • Direct effect of rotations on rhizosphere P content and P cycling gene abundance. [ABSTRACT FROM AUTHOR]

In the present study, four continuous industrial-scale microalgae reactors were evaluated regarding microalgal and microbial species composition and characteristics of the biomass produced. The results showed that complex patterns of species succession occurred in all reactors, being influenced by culture medium (synthetic medium or domestic wastewater), contamination, environmental variables and surface to volume ratio. Over time, the inoculated target species, Scenedesmus almeriensis , was gradually replaced by other green algae in raceway type reactors (RW) and by filamentous cyanobacteria in the thin layer cascade reactor (TL). The highest dry biomass was recorded in the TL, reaching 2.6 g L−1, and did not exceed 0.9 g L−1 in all RW. In general, the carbon, nitrogen, protein and lipid contents in the biomass were higher in outdoor RW, followed by TL and then by indoor RW. Carbohydrates and carotenoids did not show significant differences between the reactors and chlorophyll values followed the same pattern as dry mass. The microbiome which was analyzed only in the outdoor RW reactors sensitively reflected environmental and chemical variations, presenting a diverse composition and relevant quantitative importance in the biomass. Despite this, the chemical and biochemical characteristics of the biomass were similar to those obtained in typical algal cultures of higher purity, proving to be suitable for various uses such as biofertilizers or biofuels. The results reinforce that industrial microalgal cultures are microbial consortia and knowing their composition and succession as well as the possible manipulation of their composition, are strategic challenges for the technical and economic viability of industrial production of microalgae. • Industrial scale reactors showed complex algal and microbial species succession. • Growth and biomass were similar in cultures using wastewater and synthetic media. • Even with contamination, biomass features remained within expected for algal cultivation. • Metagenomic analysis is useful for culture monitoring and process management. [ABSTRACT FROM AUTHOR]

New scientific techniques and methods are always needed to link the perpetrators to the incident or the crime scene. Recent microbiota studies based on NGS (Next-generation sequencing) show that various biological samples from crime scenes have the potential to be used in forensic investigations. Especially when DNA traces belonging to more than one person are insufficient to fully determine the genetic profile, a secret sample, such as a microbiota sample created by the suspect's touch, can be used. In this preliminary study, a fictionalized experimental model was designed to investigate the transfer and persistence of the hand microbiome on the knife handle, which has a high potential to be used in criminal incidents, by metagenomic analysis methods. In addition, it was aimed to determine the transfer of specific bacterial species identified only to the person among the five participants onto the knife handle and their persistence over time. In the first stage of the research, samples were collected from the hands of 5 volunteer participants using the swap method, including their palms. Then, after each participant held a different knife, samples were collected from the knife handles via swabs from different angles of the knives at 4 and 24 h and analyzed by metagenomic methods. The findings of this preliminary study showed that the heatmap graphs generated after UniFrac distance analysis were not successful in establishing any similarity between the hand samples and the post-transfer knife handle samples. Nonetheless, it was observed that the transfer of bacterial species detected in the hand samples to knives differed according to the individuals and some bacterial species were transferred to the knife samples held by the participants. The number of bacterial species detected that are specific to each participant's hand sample was 302 in total, and it was determined that a total of 8.28 % of these bacterial species were transferred to the knife handle samples of the 4th hour and 6.95 % to the knife samples of the 24th hour. In the presented study, considering the transfer of some bacterial species in the hand microbiome, which are effective in the variation between individuals, onto the knife; It has been evaluated that some rare bacterial species can be important potential markers to associate the object with the perpetrator. • The transfer and persistence of the hand microbiome onto the knife handle was investigated by metagenomic analysis. • The transfer of bacterial species from hand samples to knives varies from person to person. • The transfer of specific bacterial species from the participants' hand samples to the 4th hour knife handle samples was higher than the 24th hour samples. • Some rare bacterial species in the hand microbiome are important for associating the object with the perpetrator. [ABSTRACT FROM AUTHOR]

Pathogenic microorganisms can adhere to the surfaces of water conducting systems, finally resulting in biofilm structures. Considering the importance of the adhesion capability of cells and the biofilm formation in these surfaces, their inhibition by using naturally occurring antimicrobial compounds can be a potential alternative or complement to water chlorination. This work aimed to study the antiadhesive capability of vanillin-functionalized stainless-steel surfaces against bacteria present in low-pressure water distribution network. Stainless-steel surfaces were pretreated (by sanding or polishing) and activated, allowing the covalent anchoring of vanillin to the stainless-steel. Characterization of functionalized surfaces, by macroscopic, microscopic, and elemental analysis confirmed the efficiency of the vanillin anchoring protocol. Subsequently, in vitro antiadhesive capability assays were performed with Staphylococcus epidermidis as a model microorganism to assess the antiadhesiveness capacity of the functionalized surfaces. This assay allowed the confirmation of the capacity of vanillin-functionalized surfaces to prevent the adhesion of S. epidermidis to the stainless-steel surfaces. Finally, grates were functionalized and placed in low-pressure water conduction pipes in the city of Valencia, Spain. After placement, samples of the biofilm adhered to the grates were taken at certain times and analyzed through metagenomic analysis. The results showed statistically significant differences in both the amount and type of bacterial strains adhered to vanillin-functionalized and non-functionalized grates. These findings demonstrated for the first time the potential application of vanillin-functionalized stainless-steel surfaces in water conduction systems to avoid the adhesive ability of bacteria, preventing their contamination and/or biofilm formation. [Display omitted] • Vanillin-functionalization inhibits adhesion of S. epidermidis to stainless steel surfaces. • Functionalized grates reduced biofilm variability and bacterial concentration. • The effect of functionalization is highly dependent on the bacterial genus. • Vanillin enhances stainless-steel grates' anti-biofilm properties in water networks. [ABSTRACT FROM AUTHOR]

Low temperatures could inhibit the activity of anaerobic ammonium oxidizing bacteria (AnAOB). This study investigated the effect of exogenous zero-valent iron (ZVI) on Anammox-hydroxyapatite (HAP) system at 17 ± 1 °C. The results showed that long-term addition of ZVI increased the nitrogen removal efficiency by 8.59 %, and alleviated the inhibition of AnAOB under the condition of low temperature. After addition of ZVI, the activity of AnAOB and the heme c content increased by 58.20 % and 4.83 %, respectively. Moreover, the functional enzyme activities of NIR, HZS, and HZO increased by 94.12 %, 36.36 %, and 16.67 %, respectively. The concentrations of quorum sensing molecules, i.e., C 6 -HSL and C 8 -HSL, increased by 191.17 % and 41.54 %, respectively, after ZVI addition. Metagenomic analysis revealed that the addition of 5 g/L ZVI stimulated the relative abundance of Fe(II) metabolism-related genes in AnAOB at 17 ± 1 °C, thereby contributing to the uptake, transport, utilization, and storage of Fe(II). In summary, the addition of ZVI could improve the nitrogen removal performance of the anammox-HAP system at the low temperature. [Display omitted] • 5 g/L ZVI promoted the nitrogen removal performance of Anammox-HAP system at 17°C. • Microbial quorum sensing was enhanced after ZVI addition under low-temperature shock. • ZVI could enhance utilization, transport, utilization, and storage of Fe(II) in anammox consortia. [ABSTRACT FROM AUTHOR]

Mine drainage waters often contain elevated concentrations of toxic metals and can be a source of environmental pollution. Manganese (Mn)-oxidizing bacteria (MnOB), which can oxidize soluble Mn(II) to insoluble Mn(III, IV) under neutral pH conditions, are expected to be a promising biological agent in passive mine drainage remediation. However, the diversity, functionality and applicability of MnOB for mine drainage treatment remain mostly unknown. Given that many mine environments are poor in organic substances, it is necessary to elucidate the functions of MnOB communities that contribute to metal removal without supplementation with extra organic matter. Here, we constructed in situ continuous-flow bioreactors for treating mine drainage containing approximately 20 mg L−1 Mn(II) and 6 mg L−1 zinc (Zn) (II) and operated these bioreactors without amended organic matter. The removal of Mn(II) and Zn(II) ions reached more than 98 % at a hydraulic retention time of 0.5 days. The X-ray diffraction pattern of Mn oxides deposited on the surface of limestone carriers indicated woodruffite-like mineral accumulation in the reactors. Several heterotrophic MnOB were isolated from the bioreactor, and metagenomic analysis revealed a predominance of diverse lineages of heterotrophs, including Elusimicrobiota , which harbored MoxA-like multicopper oxidase genes. Furthermore, the metagenomic analysis also suggested the involvement of gammaproteobacterial species that possessed putative genes for extracellular electron uptake and CO 2 fixation. Our findings offer the first insights into the potential for chemolithoautotrophic Mn(II) oxidation processes via electron transfer from Mn(II/III) and application of chemolithoautotrophic and heterotrophic MnOB in mine drainage remediation without supplying organic materials. [Display omitted] • In situ continuous-flow pilot-scale bioreactors were operated for mine drainage. • The bioreactors achieved over 98 % removal of Mn(II) and Zn(II) without organic substrates. • Biogenic manganese oxides were precipitated in the bioreactor systems. • Chemolithotrophic and heterotrophic Mn(II/III)-oxidizers may drive Mn removal. [ABSTRACT FROM AUTHOR]

Nitrate and Cr(VI) are the typical and prevalent co-contaminants in the groundwater, how to synchronously and effectively diminish them has received growing attention. The most problem that currently limits the nitrate and Cr(VI) reduction technology for groundwater remediation is with emphasis on exploring the optimal electron donors. This study investigated the feasibility of utilizing the synergistical effect of inorganic electron donors (pyrite, sulfur) and inherently limited organics to promote synchronous nitrate and Cr(VI) removal, which meets the requirement of naturally low-carbon and eco-friendly technologies. The NO 3 −-N and Cr(VI) removal efficiencies in the pyrite and sulfur involved mixotrophic biofilter (PS–BF: approximately 90.8 ± 0.6% and 99.1 ± 2.1%) were substantially higher than that in a volcanic rock supported biofilter (V–BF: about 49.6% ± 2.8% and 50.0% ± 9.3%), which was consistent with the spatial variations of their concentrations. Abiotic and biotic batch tests directly confirmed the decisive role of pyrite and sulfur for NO 3 −-N and Cr(VI) removal via chemical and microbial pathways. A server decline in sulfate production correlated with decreasing COD consumption revealed that there was sulfur disproportionation induced by limited organics. Metagenomic analysis suggested that chemoautotrophic microbes like Sulfuritalea and Thiobacillus were key players responsible for sulfur oxidation, nitrate and Cr(VI) reduction. The metabolic pathway analysis suggested that genes encoding functional enzymes related to complete denitrification, S oxidation, and dissimilatory sulfate reduction were upregulated, however, genes encoding Cr(VI) reduction enzymes (e.g. chrA , chrR , nemA , and azoR) were downregulated in PS-BF, which further explained the synergistical effect of multiple electron donors. These findings provide insights into their potential cooperative interaction of multiple electron donors on greatly promoting nitrate and Cr(VI) removal and have implications for the remediation technology of nitrate and Cr(VI) co-contaminated groundwater. [Display omitted] • PS-BF exhibited superior and stable removal efficiencies of NO 3 −-N and Cr(VI). • The synergistic effect among pyrite, sulfur and organics was verified. • A higher content of deposited Cr(III) occurred in PS-BF system. • Autotroph like Sulfuritalea and Thiobacillus were players for N and Cr(VI) removal. • Functional genes for C, S, Fe, N, Cr cycles differed in two systems. [ABSTRACT FROM AUTHOR]