Predicting the Functional Potential of the Microbiome from Marker Genes Using PICRUSt

Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing

Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.

Differentiation and response mechanisms of the endophytic flora of plants ecologically restored in the ilmenite area

Heavy metal contamination in soil is a serious environmental challenge, and abandoned mining areas are of particular concern. In order to rehabilitate the ecology of these areas. In this study, we used ICP-MS and potentiometric method to analyze the soil physicochemical and then endophytic bacteria of remediation plants with the help of 16sRNA sequencing, in order to investigate the ecological remediation of abandoned ilmenite mine and the effect of soil microbiology by seven common plants. The results revealed that the abandonment of ilmenite significantly increased the contents of total phosphorus, total potassium, available potassium, iron, and lead in the surrounding soils. It also affected the richness and diversity of endophytic bacterial communities. Pvi had the highest richness, while Tsi had the lowest richness (P < 0.05). A total of 28 phyla, 69 classes, 171 orders, and 521 genera were identified. A total of nine core OTUs were found: Stenotrophomonas, Chryseobacterium, Lactobacillus, Clostridium_sensu_stricto_12, Prevotella, Lactobacillus, Bradyrhizobium, Nocardioides, and Delftia. Beta diversity analysis revealed that the community structure of the endophytic bacteria differed during the remediation process at the ilmenite site. Functional prediction revealed upregulation of Dco transporter protein function, DNA-binding transcriptional regulators, glyoxalase or related metal-dependent hydrolases, acyl coenzyme A synthetases, ATPase components, amino acid synthesis, and cellular respiration-related functions. Pearson correlation analysis revealed that the SOC, TK, AN, AK, and Zn contents were significantly correlated with α diversity. Redundancy analysis (RDA) revealed that Actinobacteriota was significantly positively correlated with soil SOD, AN, TN, and TK contents. For the first time, this study revealed the interactions among plants, endophytic bacteria and soil pollutants, laying a theoretical basis for screening specific plant endophytic bacteria for ecological restoration.

Survey of gut microbial biogeography and their functional niche in the grow-finishing swine of ordinary feeding

Background

Swine represent one of the most economically significant livestock worldwide, and their intestinal microbial communities are crucial for maintaining physiological development and regulating host metabolism. While extensive research has focused on the fecal microbiota of swine, investigations into microbial communities across different intestinal segments remain limited.

Objective

This study aims to elucidate the intestinal microbiota of swine by analyzing luminal contents from different intestinal segments, including the duodenum, jejunum, ileum, cecum, and colon.

Methods

We employed 16S rRNA sequencing to explore the diversity and structure of gut microbial biogeography, microbial functional niches, and their associated pathways.

Results

Our findings reveal significantly lower microbial richness and diversity in the small intestine (duodenum, jejunum, and ileum) compared to the large intestine (cecum and colon) (p < 0.05). At the phylum level, Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant phyla, collectively accounting for over 90% of the total sequences. In the small intestine, Proteobacteria (4.76-34.2%), Actinobacteria, and Fusobacteriota were more abundant, whereas in the large intestine, Firmicutes (89.8-90.4%) was predominated. At the genus level, Fusobacterium, Corynebacterium, Rothia, Bradyrhizobium, and Brevundimonas were predominant in duodenum. Romboutsia, Clostridium_sensu_stricto_1, Terrisporobacter, and Jeotgalicoccus demonstrated greater abundances in the jejunum and ileum. Oscillospiraceae_UCG-005 in the cecum and Christensenellaceae_R-7_group in the colon were more abundant with 16.4 and 20.2% relative abundances, respectively. The specialists detected from the duodenum to the colon were all the predominant genera in each intestinal segment with relatively higher relative abundance. For instance, Romboutsia (3.06-36.1%), Clostridium_sensu_stricto_1 (5.31-18.6%), and Terrisporobacter (0.849-5.72%) were dominant genera and specialists in the small intestine, associated with enriched pathways of Amino acid metabolism and Lipid metabolism. Conversely, Oscillospiraceae_UCG-005 (16.4%, 4.06%) and Christensenellaceae_R-7_group (5.44%, 20.2%) are predominant genera and specialists within the large intestine, linked to pathways involved in Glycan biosynthesis and metabolism pathway, as well as the Biosynthesis of other secondary metabolites.

Conclusion

These highlight the importance of genus specialists compared to genus generalists. The findings provide essential data for assessing the role of the intestinal microbiome in maintaining and enhancing swine health and productivity, offering fundamental guidance for further exploration of host-microbe interaction mechanisms and regulatory pathways.

Gut microbiota and functional metabolic predictions in white feces disease-infected Pacific white shrimp, Penaeus vannamei, from Indonesian farms

The etiological agent of white feces disease (WFD) infecting Pacific white shrimp Penaeus vannamei in Indonesia farms remains obscure. The present study aimed to identify possible causative agents of WFD infection in Pacific white shrimps cultured in Indonesian farms. WFD-infected and healthy samples (shrimp gut and rearing water) were collected from 8 commercial shrimp farms in East Java, Indonesia followed by bacterial community profiling using HiSeq sequencing of 16S rRNA gene amplicons. The results showed that the microbiota composition in the guts of WFD-infected shrimps was significantly different (p < 0.05) from the guts of healthy shrimps in term of genus and bacterial species. The intestinal bacterial communities of WFS-infected shrimps were overrepresented by Vibrio coralliilyticus, whereas Paracoccus was underrepresented. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States functional predictions indicated that relative abundances of 12 genes associated with the pathogenicity of bacteria including amino acid metabolisms, carbohydrate metabolisms, glycan biosynthesis, and xenobiotic biodegradation and metabolism were significantly (p < 0.05) higher in the gut microbiota of WFD-infected shrimps. These findings provide insights into the microbiome domination and their metabolic activities in the digestive tract of WFD-infected shrimps and suggest that V. coralliilyticus is a possible causative agent of WFD in cultured Indonesia Pacific white shrimp.

The bidirectional interaction between antidepressants and the gut microbiota: are there implications for treatment response?

This review synthesizes the evidence on associations between antidepressant use and gut microbiota composition and function, exploring the microbiota's possible role in modulating antidepressant treatment outcomes. Antidepressants exert an influence on measures of gut microbial diversity. The most consistently reported differences were in β-diversity between those exposed to antidepressants and those not exposed, with longitudinal studies supporting a potential causal association. Compositional alterations in antidepressant users include an increase in the Bacteroidetes phylum, Christensenellaceae family, and Bacteroides and Clostridium genera, while a decrease was found in the Firmicutes phylum, Ruminococcaceae family, and Ruminococcus genus. In addition, antidepressants attenuate gut microbial differences between depressed and healthy individuals, modulate microbial serotonin transport, and influence microbiota's metabolic functions. These include lyxose degradation, peptidoglycan maturation, membrane transport, and methylerythritol phosphate pathways, alongside gamma-aminobutyric acid metabolism. Importantly, baseline increased α-diversity and abundance of the Roseburia and Faecalibacterium genera, in the Firmicutes phylum, are associated with antidepressant response, emerging as promising biomarkers. This review highlights the potential for gut microbiota as a predictor of treatment response and emphasizes the need for further research to elucidate the mechanisms underlying antidepressant-microbiota interactions. More homogeneous studies and standardized techniques are required to confirm these initial findings.

The symbiont Wolbachia increases resistance to bifenthrin in Ectropis grisescens by regulating the host detoxification function

The global issue of insecticide resistance among pests is a major concern. Ectropis grisescens Warren (Lepidoptera: Geometridae), is a highly destructive leaf-eating pest distributed in tea plantations throughout China and Japan, and has exhibited resistance to various insecticides. Recent studies suggest that insect symbionts play a role in influencing insecticide resistance, however, their specific involvement in E. grisescens remains unclear. Here, we initially selected appropriate antibiotic mixtures at a concentration of 300 μg ml-1. The bioassay results showed that the insecticide susceptibility of the E. grisescens population treated with antibiotic mixtures significantly increased exposed to bifenthrin. Comparative analysis revealed that the LC50 value, survival rate, P450 enzyme activity, and relative content of Wolbachia in the E. grisescens population treated with 300 μg ml-1 tetracycline were notably lower than those treated with other antibiotics (ampicillin, gentamicin, and streptomycin). Moreover, the population treated with 2.5 mg ml-1 tetracycline exhibited even greater reductions in these parameters than the 300 μg ml-1 tetracycline-treated group. Additionally, 16S rRNA sequencing results showed a significant decrease in xenobiotics metabolism by cytochrome P450 in the E. grisescens population treated with 2.5 mg ml-1 tetracycline. Transcriptome analysis showed a significant down-regulation of two cytochrome P450 genes in E. grisescens population without Wolbachia. These results suggest that Wolbachia may contribute to the resistance of E. grisescens to bifenthrin by regulating cytochrome P450 genes, providing a foundation for further study on the mechanism of symbiont-mediated host detoxification metabolism in insect pests.

Towards AI-designed genomes using a variational autoencoder

Genomes encode elaborate networks of genes whose products must seamlessly interact to support living organisms. Humans' capacity to understand these biological systems is limited by their sheer size and complexity. In this article, we develop a proof of concept framework for training a machine learning (ML) algorithm to model bacterial genome composition. To achieve this, we create simplified representations of genomes in the form of binary vectors that indicate the encoded genes, henceforth referred to as genome vectors. A denoising variational autoencoder was trained to accept corrupted genome vectors, in which most genes had been masked, and reconstruct the original. The resulting model, DeepGenomeVector, effectively captures complex dependencies in genomic networks, as evaluated by both qualitative and quantitative metrics. An in-depth functional analysis of a generated genome vector shows that its encoded pathways are interconnected, near complete, and ecologically cohesive. On the test set, where the model's ability to reconstruct uncorrupted genome vectors was evaluated, Area Under the Receiver Operating Curve (AUROC) and F1 scores of 0.98 and 0.83, respectively, support the model's strong performance. This article showcases the power of ML approaches for synthetic biology and highlights the possibility that artifical intelligence agents may one day be able to design genomes that animate carbon-based cells.

Unveiling methane oxidation dynamics, microbial community, and function of Fe(III)-driven anaerobic methane oxidation inside landfill

Trivalent iron (Fe3+) could participate in methane (CH4) oxidation as an electron acceptor under anaerobic conditions, but the kinetic process remains unknown in landfills, and the understanding of metabolic pathway of Fe3+-dependent anaerobic methane oxidation (Fe-DAMO) is still limited. In this study, the dual-substrate (CH4-Fe3+) kinetic model of CH4 oxidation is obtained with Vmax (7.35 ± 0.4184)μmol/(kg d), half-saturation constant K m , CH 4 (16.6699 ± 2.3940)ppmv, and K m , Fe 3 + (0.00107 ± 0.0002g/g). Microbial community analysis shows that Methanobacteriales and Clostridia are dominant microorganisms of Fe-DAMO. PICRUSt analysis confirms that the metabolic pathway of AMO is the reverse CH4 production pathway. The results provide a new perspective for CH4 biodegradation in landfills and offer a better understanding of Fe-DAMO process.

The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants

Introduction

Thus far, the impact of kaolin mining activities on the surrounding native plants and rhizosphere microecology has not been fully understood.

Methods

In this study, we used 16S rRNA high-throughput sequencing to examine the impact of kaolin mining on the rhizosphere bacterial communities and functions of three local plant species: Conyza bonariensis, Artemisia annua, and Dodonaea viscosa.

Results

The results showed that kaolin mining significantly reduced the diversity of rhizosphere bacteria in these plants, as indicated by the Shannon, Simpson, Chao1, and observed species indices (p < 0.05). Kaolin mining had an impact on the recruitment of three rhizosphere bacteria native to the area: Actinoplanes, RB41, and Mycobacterium. These bacteria were found to be more abundant in the rhizosphere soil of three local plants than in bulk soil, yet the mining of kaolin caused a decrease in their abundance (p < 0.05). Interestingly, Ralstonia was enriched in the rhizosphere of these plants found in kaolin mining areas, suggesting its resilience to environmental stress. Furthermore, the three plants had different dominant rhizosphere bacterial populations in kaolin mining areas, such as Nocardioides, Pseudarthrobacter, and Sphingomonas, likely due to the unique microecology of the plant rhizosphere. Kaolin mining activities also caused a shift in the functional diversity of rhizosphere bacteria in the three local plants, with each plant displaying different functions to cope with kaolin mining-induced stress, such as increased abundance of the GlpM family and glucan-binding domain.

Discussion

This study is the first to investigate the effects of kaolin mining on the rhizosphere microecology of local plants, thus contributing to the establishment of soil microecological health monitoring indicators to better control soil pollution in kaolin mining areas.

Microbiomes of three coral species in the Mexican Caribbean and their shifts associated with the Stony Coral Tissue Loss Disease

Stony Coral Tissue Loss Disease (SCTLD) has caused widespread coral mortality in the Caribbean Region. However, how the disease presence alters the microbiome community, their structure, composition, and metabolic functionality is still poorly understood. In this study, we characterized the microbial communities of the tissues of apparently healthy and diseased SCTLD colonies of the species Siderastrea siderea, Orbicella faveolata, and Montastraea cavernosa to explore putative changes related to the presence of SCTLD. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia were the best represented classes in the healthy tissues of all coral species, and alpha diversity did not show significant differences among the species. The microbial community structure between coral species was significantly different (PERMANOVA: F = 3.46, p = 0.001), and enriched genera were detected for each species: Vibrio and Photobacterium in S. siderea, Spirochaeta2 and Marivivens in O. faveolata and SAR202_clade and Nitrospira in M. cavernosa. Evidence of SCTLD in the microbial communities was more substantial in S. siderea, where differences in alpha diversity, beta diversity, and functional profiles were observed. In O. faveolata, differences were detected only in the community structure, while M. cavernosa samples showed no significant difference. Several microbial groups were found to have enriched abundances in tissue from SCTLD lesions from S. siderea and O. faveolata, but no dominant bacterial group was detected. Our results contribute to understanding microbial diversity associated with three scleractinian coral species and the shifts in their microbiomes associated with SCTLD in the Mexican Caribbean.

Different Prostatic Tissue Microbiomes between High- and Low-Grade Prostate Cancer Pathogenesis

Numerous human pathologies, such as neoplasia, are related to particular bacteria and changes in microbiome constituents. To investigate the association between an imbalance of bacteria and prostate carcinoma, the microbiome and gene functionality from tissues of patients with high-grade prostate tumor (HGT) and low-grade prostate tumor (LGT) were compared utilizing next-generation sequencing (NGS) technology. The results showed abnormalities in the bacterial profiles between the HGT and LGT specimens, indicating alterations in the make-up of bacterial populations and gene functionalities. The HGT specimens showed higher frequencies of Cutibacterium, Pelomonas, and Corynebacterium genera than the LGT specimens. Cell proliferation and cytokine assays also showed a significant proliferation of prostate cancer cells and elevated cytokine levels in the cells treated with Cutibacterium, respectively, supporting earlier findings. In summary, the HGT and LGT specimens showed differences in bacterial populations, suggesting that different bacterial populations might characterize high-grade and low-grade prostate malignancies.

Effects of uranium mining on the rhizospheric bacterial communities of three local plants on the Qinghai-Tibet Plateau

In this study, we used 16S high-throughput sequencing to investigate the effects of uranium mining on the rhizospheric bacterial communities and functions of three local plant species, namely, Artemisia frigida, Acorus tatarionwii Schott., and Salix oritrepha Schneid. The results showed that uranium mining significantly reduced the diversity of rhizospheric bacteria in the three local plant species, including the Shannon index and Simpson index (P < 0.05). Interestingly, we found that Sphingomonas and Pseudotrichobacter were enriched in the rhizosphere soil of the three local plants from uranium mining areas, indicating their important ecological role. The three plants were enriched in various dominant rhizospheric bacterial populations in the uranium mining area, including Vicinamidobacteriaceae, Nocardioides, and Gaiella, which may be related to the unique microecological environment of the plant rhizosphere. The rhizospheric bacterial community of A. tatarionwii plants from tailings and open-pit mines also showed a certain degree of differentiation, indicating that uranium mining is the main factor driving the differentiation of plant rhizosphere soil communities on the plateau. Functional prediction revealed that rhizospheric bacteria from different plants have developed different functions to cope with stress caused by uranium mining activities, including enhancing the translational antagonist Rof, the translation initiation factor 2B subunit, etc. This study explores for the first time the impact of plateau uranium mining activities on the rhizosphere microecology of local plants, promoting the establishment of effective soil microecological health monitoring indicators, and providing a reference for further soil pollution remediation in plateau uranium mining areas.

An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease

Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs. non-CF) and bacterial diversity, based on previously performed small subunit rRNA sequencing data. Proteins from each pooled sample group were digested and subjected to liquid chromatography tandem mass spectrometry (MS/MS). MS/MS spectra were matched to human and bacterial peptide sequences leveraging a bioinformatic workflow using a metagenomics-guided protein sequence database and rigorous evaluation. Label-free quantification revealed differentially abundant human peptides from proteins with known roles in CF, like neutrophil elastase and collagenase, and proteins with lesser-known roles in CF, including apolipoproteins. Differentially abundant bacterial peptides were identified from known CF pathogens (e.g., Pseudomonas), as well as other taxa with potentially novel roles in CF. We used this host-microbe peptide panel for targeted parallel-reaction monitoring validation, demonstrating for the first time an MS-based assay effective for quantifying host-microbe protein dynamics within BAL cells from individual CF patients. Our integrated bioinformatic and analytical workflow combining discovery, verification, and validation should prove useful for diverse studies to characterize microbial contributors in airway diseases. Furthermore, we describe a promising preliminary panel of differentially abundant microbe and host peptide sequences for further study as potential markers of host-microbe relationships in CF disease pathogenesis.IMPORTANCEIdentifying microbial pathogenic contributors and dysregulated human responses in airway disease, such as CF, is critical to understanding disease progression and developing more effective treatments. To this end, characterizing the proteins expressed from bacterial microbes and human host cells during disease progression can provide valuable new insights. We describe here a new method to confidently detect and monitor abundance changes of both microbe and host proteins from challenging BAL samples commonly collected from CF patients. Our method uses both state-of-the art mass spectrometry-based instrumentation to detect proteins present in these samples and customized bioinformatic software tools to analyze the data and characterize detected proteins and their association with CF. We demonstrate the use of this method to characterize microbe and host proteins from individual BAL samples, paving the way for a new approach to understand molecular contributors to CF and other diseases of the airway.

Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity

Coumarin, a phenolic compound, is a secondary metabolite produced by plants such as Tanga and Lime. Coumarin derivatives were prepared via Pechmann condensation. In this study, we performed in vitro and in vivo experiments to determine the antimicrobial and gut immune-regulatory functions of coumarin derivatives. For the in vitro antimicrobial activity assay, coumarin derivatives C1 and C2 were selected based on their pathogen-killing activity against various pathogenic microbes. We further demonstrated that the selected coumarin derivatives disrupted bacterial cell membranes. Next, we examined the regulatory function of the coumarin derivatives in gut inflammation using an infectious colitis model. In an in vivo infectious colitis model, administration of selected C1 coumarin derivatives reduced pathogen loads, the number of inflammatory immune cells (Th1 cells and Th17 cells), and inflammatory cytokine levels (IL-6 and IL-1b) in the intestinal tissue after pathogen infection. In addition, we found that the administration of C1 coumarin derivatives minimized abnormal gut microbiome shift-driven pathogen infection. Potential pathogenic gut microbes, such as Enterobacteriaceae and Staphylococcaceae, were increased by pathogen infection. However, this pathogenic microbial expansion was minimized and beneficial bacteria, such as Ligilactobacillus and Limosilactobacillus, increased with C1 coumarin derivative treatment. Functional gene enrichment assessment revealed that the relative abundance of genes associated with lipid and nucleotide metabolism was reduced by pathogen infection; however, this phenomenon was not observed in C1 coumarin derivative-treated animals. Collectively, our data suggest that C1 coumarin derivative is effective antibacterial agents that minimize pathogen-induced gut inflammation and abnormal gut microbiome modulation through their antibacterial activity.

Exploring the root canal microbiome in previously treated teeth: A comparative study of diversity and metabolic pathways across two geographical locations

AIM

To analyse and compare the root canal microbiome present in root-filled teeth of two different geographical populations, and to study their functional potential using a next-generation sequencing approach.

METHODOLOGY

Sequencing data obtained from surgical specimens from previously treated teeth with periapical bone loss from Spain and USA were included in the study. Taxa were classified using SILVA v.138 database. Differences in genera abundances among the 10 most abundant genera were evaluated using a Kruskal-Wallis test. Alpha diversity indices were calculated in mothur. The Shannon and Chao1 indices were used. Analyses of similarity (ANOSIM) to determine differences in community composition were done in mothur, with Bonferroni correction for multiple comparisons. p-Values < .05 were considered statistically significant. Identification of enriched bacteria function prediction in the study groups (KEGG pathways) was carried out by linear discriminant analysis effect size (LEfSe) via Python 3.7.6.

RESULTS

A greater alpha-diversity (Shannon and Chao1 indices) was observed from samples obtained in Spain (p = .002). Geography showed no significant effects on community composition via an ANOSIM using Bray-Curtis dissimilarities (R = 0.03, p = .21). Bacterial functional analysis prediction obtained by PICRUSt showed that 5.7% KEGG pathways differed between the Spain and US samples.

CONCLUSIONS

The taxonomic assessment alone does not fully capture the microbiome's differences from two different geographical locations. Carbohydrate and amino acid metabolism were enriched in samples from Spain, while samples from USA had a higher representation of pathways related to nitrogen, propanoate metabolism, and secretion systems.

Identification of keystone taxa in root canals and periapical lesions of post-treatment endodontic infections: Next generation microbiome research

AIM

The aim of this study was to analyse and compare the microbiome present in root canals and periapical lesions of teeth with post-treatment infections, and to identify the presence of keystone taxa in both habitats using next-generation sequencing analysis.

METHODOLOGY

Apices and periapical lesions of patients with post-treatment apical periodontitis were surgically extracted. Specimens were cryo-pulverized, bacterial DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced using the Illumina Miseq platform. Bioinformatic analysis was carried out with Mothur software, whilst diversity indices were obtained using operational taxonomic units (OTUs). The diversity indices were compared with the Kruskal-Wallis test, and community composition differences were explored with Permutational Multivariate Analysis of Variance (PERMANOVA). A bacterial functional study was performed with the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. Co-occurrence network analyses were performed using the Sparse Correlations for Compositional data (SparCC). Eigencentrality, clr-based abundance and ubiquitousness were applied to infer keystone taxa. P values <.05 were considered statistically significant.

RESULTS

Thirty-two apices and thirty-nine periapical lesions were sequenced and analysed. A similar alpha-diversity (p < .05) and community composition (p = .91) was observed for apices and lesion samples. The most abundant OTUs identified amongst all samples included Fusobacterium nucleatum, Prevotella loescheii, Streptococcus intermedius, Porphyromonas gingivalis, Parvimonas micra, Synergistetes bacterium, Tannerella forsythia and Peptostreptococcus stomatis. The metabolic pathways with >0.81% abundances included membrane transport, genetic information processing and metabolic pathways. F. nucleatum was identified as a keystone taxon as it showed ubiquitousness, an eigenvector centrality value of 0.83 and a clr-based abundance >4.

CONCLUSIONS

The microbiome in apices and periapical lesions of post-treatment endodontic infections showed a similar diversity and taxonomic composition. Co-occurrence network analyses at OTU level identified F. nucleatum as a keystone taxon candidate in these infections.

Multi-omics unveils tryptophan metabolic pathway as a key pathway influencing residual feed intake in Duroc swine

The genetic trait of residual feed intake (RFI) holds considerable importance in the swine industry. Recent research indicates that the gut microbiota of pigs plays a pivotal role in the manifestation of the RFI trait. Nevertheless, the metabolic pathways involved in the functioning of these microorganisms remain elusive. Thus, based on the ranking of the RFI trait in Duroc pigs, the present study selected the top 10 and bottom 10 pigs as the experimental subjects. The distribution and metabolite differences of cecal microbiota were analyzed using 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. The low RFI cecal group was named LRC, and the high RFI cecal group was named HRC. The results indicate that the LRC group had lower RFI, feed conversion ratio (FCR), average daily feed intake (ADFI) (p < 0.001), and thinner backfat (p < 0.05) compared with the HRC group. We simultaneously recorded the foraging behavior as well, the LRC group had a significant increase in total time spent at the feeder per day (TPD) (p < 0.05) and a significant increase in average feed intake per mins (AFI) and the number of visits to the feeder per day (NVD) compared to the HRC group (p < 0.001). Clostridium_XVIII, Bulleidia, and Intestinimonas were significantly enriched in the LRC group (p < 0.01), while Sutterella, Fusobacterium, and Bacteroides were significantly increased in the HRC group (p < 0.01). In the metabolome, we detected 390 (248 metabolites up and 142 down in the LRC compared with HRC), and 200 (97 metabolites up and 103 down in the LRC compared with HRC) differential metabolites in positive and negative ionization modes. The comprehensive analysis found that in the LRC group, Escherichia and Eubacterium in the gut may increase serotonin content, respectively. Bacteroides may deplete serotonin. We suggest that the RFI may be partly achieved through tryptophan metabolism in gut microbes. In individuals with low RFI, gut microbes may enhance feed efficiency by enhancing host synthesis and metabolism of tryptophan-related metabolites.

Bioaugmentation of anaerobic digesters with the enriched lignin-degrading microbial consortia through a metagenomic approach

The recalcitrance of lignin impedes the efficient utilization of lignocellulosic biomass, hindering the efficient production of biogas and value-added materials. Despite the emergence of anaerobic digestion as a superior alternative to the aerobic method for lignin processing, achieving its feasibility requires thorough characterization of lignin-degrading anaerobic microorganisms, assessment of their biomethane production potential, and a comprehensive understanding of the degradation pathway. This study aimed to address the aforementioned necessities by bioaugmenting seed sludge with three distinct enriched lignin-degrading microbial consortia at both 25 °C and 37 °C. Enhanced biomethane yields was detected in the bioaugmented digesters, while the highest production was observed as 188 mLN CH4 gVS-1 in digesters operated at 37 °C. Moreover, methane yield showed a significant improvement in the samples at 37 °C ranging from 110% to 141% compared to the control, demonstrating the efficiency of the enriched lignin-degrading microbial community. Temperature and substrate were identified as key factors influencing microbial community dynamics. The observation that microbial communities tended to revert to the initial state after lignin depletion, indicating the stability of the overall microbiota composition in the digesters, is a promising finding for large-scale studies. Noteworthy candidates for lignin degradation, including Sporosarcina psychrophila, Comamonas aquatica, Shewanella baltica, Pseudomonas sp. C27, and Brevefilum fermentans were identified in the bioaugmented samples. PICRUSt2 predictions suggest that the pathway and specific proteins involved in anaerobic lignin degradation might share similarities with those engaged in the degradation of aromatic compounds.

Transforming Big Data into AI-ready data for nutrition and obesity research

OBJECTIVE

Big Data are increasingly used in obesity and nutrition research to gain new insights and derive personalized guidance; however, this data in raw form are often not usable. Substantial preprocessing, which requires machine learning (ML), human judgment, and specialized software, is required to transform Big Data into artificial intelligence (AI)- and ML-ready data. These preprocessing steps are the most complex part of the entire modeling pipeline. Understanding the complexity of these steps by the end user is critical for reducing misunderstanding, faulty interpretation, and erroneous downstream conclusions.

METHODS

We reviewed three popular obesity/nutrition Big Data sources: microbiome, metabolomics, and accelerometry. The preprocessing pipelines, specialized software, challenges, and how decisions impact final AI- and ML-ready products were detailed.

RESULTS

Opportunities for advances to improve quality control, speed of preprocessing, and intelligent end user consumption were presented.

CONCLUSIONS

Big Data have the exciting potential for identifying new modifiable factors that impact obesity research. However, to ensure accurate interpretation of conclusions arising from Big Data, the choices involved in preparing AI- and ML-ready data need to be transparent to investigators and clinicians relying on the conclusions.

Impact of Vanadium-Titanium-Magnetite Mining Activities on Endophytic Bacterial Communities and Functions in the Root Systems of Local Plants

This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium-titanium-magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable decrease in both the biodiversity and abundance of endophytic bacteria within the root systems of Eleusine indica and Carex (p < 0.05). Significant reductions were observed in the populations of Nocardioides, concurrently with substantial increments in the populations of Pseudomonas (p < 0.05), indicating that Pseudomonas has a strong adaptability to this environmental stress. In addition, β diversity analysis revealed divergence in the endophytic bacterial communities within the roots of E. indica and Carex from the VTM mining area, which had diverged to adapt to the environmental stress caused by mining activity. Functional enrichment analysis revealed that VTM mining led to an increase in polymyxin resistance, nicotinate degradation I, and glucose degradation (oxidative) (p < 0.05). Interestingly, we found that VTM mining did not notably alter the endophytic bacterial communities or functions in the root systems of Dodonaea viscosa, indicating that this plant can adapt well to environmental stress. This study represents the primary investigation into the influence of VTM mining activities on endophytic bacterial communities and the functions of nearby plant roots, providing further insight into the impact of VTM mining activities on the ecological environment.

Effects of lactic acid bacteria inoculants on the nutrient composition, fermentation quality, and microbial diversity of whole-plant soybean-corn mixed silage

The mixture of whole-plant soybean and whole-plant corn silage (WPSCS) is nutrient balanced and is also a promising roughage for ruminants. However, few studies have investigated the changes in bacterial community succession in WPSCS inoculated with homofermentative and heterofermentative lactic acid bacteria (LAB) and whether WPSCS inoculated with LAB can improve fermentation quality by reducing nutrient losses. This study investigated the effect of Lactobacillus plantarum (L. plantarum) or Lactobacillus buchneri (L. buchneri) on the fermentation quality, aerobic stability, and bacterial community of WPSCS. A 40:60 ratio of whole-plant soybean corn was inoculated without (CK) or with L. plantarum (LP), L. buchneri (LB), and a mixture of LP and LB (LPB), and fermented for 14, 28, and 56 days, followed by 7 days of aerobic exposure. The 56-day silage results indicated that the dry matter content of the LP and LB groups reached 37.36 and 36.67%, respectively, which was much greater than that of the CK group (36.05%). The pH values of the LP, LB, and LPB groups were significantly lower than those of the CK group (p < 0.05). The ammoniacal nitrogen content of LB was significantly lower than that of the other three groups (p < 0.05), and the ammoniacal nitrogen content of LP and LPB was significantly lower than that of CK (p < 0.05). The acetic acid content and aerobic stability of the LB group were significantly greater than those of the CK, LP, and LPB groups (p < 0.05). High-throughput sequencing revealed a dominant bacteria shift from Proteobacteria in fresh forage to Firmicutes in silage at the phylum level. Lactobacillus remained the dominant genus in all silage. Linear discriminant analysis effect size (LEFSe) analysis identified Lactobacillus as relatively abundant in LP-treated silage and Weissella in LB-treated groups. The results of KEGG pathway analysis of the 16S rRNA gene of the silage microbial flora showed that the abundance of genes related to amino acid metabolism in the LP, LB, and LPB groups was lower than that in the CK group (p < 0.05). In conclusion, LAB application can improve the fermentation quality and nutritional value of WPSCS by regulating the succession of microbial communities and metabolic pathways during ensiling. Concurrently, the LB inoculant showed the potential to improve the aerobic stability of WPSCS.

Actinomycetota, a central constituent microbe during long-term exposure to diazinon, an organophosphorus insecticide

Microbial biodegradation is a primary pesticide remediation pathway. Despite diazinon is one of the most frequently used organophosphate insecticides worldwide, its effect on soil microbial community remains obscure. We hypothesize that diazinon exposure reshapes microbial community, among them increased microbes may play a crucial role in diazinon degradation. To investigate this, we collected soil from an organic farming environment, introduced diazinon, cultivated it in a greenhouse, and then assessed its effects on soil microbiomes at three distinct time points: 20, 40, and 270 days after treatment (DAT). Results from HPLC showed that the level of diazinon was gradually degraded by 98.8% at 270 DAT when compared with day zero, whereas 16S rRNA gene analysis exhibited a significant reduction in the bacterial diversity, especially at the early two time points, indicating that diazinon may exert selection pressure to the bacteria community. Here, the relative abundance of phylum Actinomycetota increased at 20 and 40 DATs. In addition, the bacterial functional gene profile employing PICRUSt2 prediction also revealed that diazinon exposure induced the genomic function related to xenobiotics biodegradation and metabolism in soil, such as CYB5B, hpaC, acrR, and ppkA. To validate if bacterial function is caused by increased relative abundance in diazinon enriched soil, further bacteria isolation resulted in obtaining 25 diazinon degradation strains out of 103 isolates. Notably, more than 70% (18 out of 25) isolates are identified as phylum Actinomycetota, which empirically confirms and correlates microbiome and PICRUSt2 results. In conclusion, this study provides comprehensive information from microbiome analysis to obtaining several bacteria isolates responsible for diazinon degradation, revealing that the phylum Actinomycetota is as a key taxon that facilitates microbial biodegradation in diazinon spoiled soil. This finding may assist in developing a strategy for microbial detoxification of diazinon, such as using an Actinomycetota rich synthetic community (SynCom).

Effects of Lonicerae flos and Turmeric extracts on growth performance and intestinal health of yellow-feathered broilers

This experiment aimed to investigate the effect of Lonicerae flos and Turmeric extracts (LTE) added to diets on growth performance and intestinal health of broilers. A total of 720 healthy 21-day-old yellow-feathered broilers were randomly divided into 3 treatment groups, with 6 replicates and 40 broilers per replicate. These 3 dietary treatments included a basal diet + 0 g/t LTE (CON), a basal diet + 300 g/t LTE (LTE300), and a basal diet + 500 g/t LTE (LTE500). The results showed that dietary supplementation of LTE linearly increased (P < 0.05) average daily gain (d 21-38) and average daily feed intake (d 21-60). At d 60, LTE300 had the highest serum total antioxidant capacity and total superoxide dismutase (P < 0.05), and LTE500 had the lowest malondialdehyde level (P < 0.05) among the three groups. Moreover, compared to CON, LTE300 significantly (P < 0.05) reduced endotoxin (d 38 and d 60) and diamine oxidase activity (d 38); LTE500 significantly (P < 0.05) reduced endotoxin (d 38 and d 60) and diamine oxidase levels (d 60) in the serum. LTE groups significantly (P < 0.05) increased ileal the ratio of villus height to crypt depth and serum immunoglobulin G. Furthermore, dietary supplementation of LTE also improved the intestinal epithelial barrier by the up-regulated mRNA expression of Claudin-1, Occludin and zonula occludens-1, and decreased the mRNA expression of interleukin-2, interleukin-8, tumor necrosis factor-α, nuclear factor κB, myeloid differentiation factor 88 and toll-like receptor 4. Compared to CON, 16S rRNA sequencing analysis showed that LTE300 had a better effect on the microbial diversity and composition in the ileum, and Bacillus and Lactobacillus_agilis were significantly enriched in LTE300. PICRUSt results showed that LTE300 was significantly (P < 0.05) enriched in four pathway pathways at KEGG level 2. In conclusion, dietary supplementation with LTE improved growth performance and intestinal health by enhancing antioxidant capacity, intestinal barrier and immune function, and regulating intestinal flora of yellow-feathered broilers.

Characteristics of microbiome-derived metabolomics according to the progression of alcoholic liver disease

BACKGROUND AND AIM

The prevalence and severity of alcoholic liver disease (ALD) are increasing. The incidence of alcohol-related cirrhosis has risen up to 2.5%. This study aimed to identify novel metabolite mechanisms involved in the development of ALD in patients. The use of gut microbiome-derived metabolites is increasing in targeted therapies. Identifying metabolic compounds is challenging due to the complex patterns that have long-term effects on ALD. We investigated the specific metabolite signatures in ALD patients.

METHODS

This study included 247 patients (heathy control, HC: n = 62, alcoholic fatty liver, AFL; n = 25, alcoholic hepatitis, AH; n = 80, and alcoholic cirrhosis, AC, n = 80) identified, and stool samples were collected. 16S rRNA sequencing and metabolomics were performed with MiSeq sequencer and liquid chromatography coupled to time-of-flight-mass spectrometry (LC-TOF-MS), respectively. The untargeted metabolites in AFL, AH, and AC samples were evaluated by multivariate statistical analysis and metabolic pathotypic expression. Metabolic network classifiers were used to predict the pathway expression of the AFL, AH, and AC stages.

RESULTS

The relative abundance of Proteobacteria was increased and the abundance of Bacteroides was decreased in ALD samples (p = 0.001) compared with that in HC samples. Fusobacteria levels were higher in AH samples (p = 0.0001) than in HC samples. Untargeted metabolomics was applied to quantitatively screen 103 metabolites from each stool sample. Indole-3-propionic acid levels are significantly lower in AH and AC (vs. HC, p = 0.001). Indole-3-lactic acid (ILA: p = 0.04) levels were increased in AC samples. AC group showed an increase in indole-3-lactic acid (vs. HC, p = 0.040) level. Compared with that in HC samples, the levels of short-chain fatty acids (SCFAs: acetic acid, butyric acid, propionic acid, iso-butyric acid, and iso-valeric acid) and bile acids (lithocholic acids) were significantly decreased in AC. The pathways of linoleic acid metabolism, indole compounds, histidine metabolism, fatty acid degradation, and glutamate metabolism were closely associated with ALD metabolism.

CONCLUSIONS

This study identified that microbial metabolic dysbiosis is associated with ALD-related metabolic dysfunction. The SCFAs, bile acids, and indole compounds were depleted during ALD progression.

CLINICAL TRIAL

Clinicaltrials.gov, number NCT04339725.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42-), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42- levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.

Exploring the influence of garlic on microbial diversity and metabolite dynamics during kimchi fermentation

Garlic (Allium sativum) is a key ingredient in Korean cuisine, particularly in the preparation of kimchi, contributing to its flavor and taste. Garlic has been a potential resource for lactic acid bacteria (LAB) in kimchi. However, the mechanism by which it influences microbial diversity and metabolite production is unclear. This study investigated the effect of garlic on the bacterial composition of and metabolite changes in kimchi. To achieve this, four separate batches of kimchi were prepared with varying garlic concentrations (w/w): 0 %, 1 %, 2 %, and 4 %, and the bacterial communities and metabolite production were monitored. In the early stages of fermentation, the count of LAB, operational taxonomic units (OTUs), and Shannon index increased linearly with the increase in garlic content. This indicated that garlic is a rich resource and contributes to the diversity of LAB during kimchi fermentation. Compared with the kimchi samples with a lower garlic content, those with a high garlic content (≥2 %) exhibited increased abundance of Lactobacillus and Leuconostoc as well as noticeable differences in functional diversity, including carbohydrate, amino acid, and energy metabolisms. Correlation analysis between sugars, organic acids, and predominant LAB in the garlic-containing kimchi samples suggested that in kimchi samples with high garlic content, LAB played a significant role in the fermentation process by metabolizing sugars and producing organic acids. Overall, this study demonstrated that the addition of garlic has a positive impact on the bacterial diversity and metabolite production during kimchi fermentation, potentially affecting the fermentation process and flavor profile of kimchi.

Effects of polystyrene microplastics on the agronomic traits and rhizosphere soil microbial community of highland barley

This study investigated the influence of polystyrene microplastics (MPs) with two different particle sizes (<1 mm, 1-5 mm) and three concentrations (1 g/m2, 10 g/m2, 50 g/m2), as well as added degrading bacteria, on the agronomic traits of highland barley and the bacterial communities in the rhizosphere soil. Results revealed that the small particle size treatment had a significant effect on reducing the 1000-grain weight of highland barley, while the large particle size treatment had an effect on reducing the spike length, width, and awn length (P < 0.05). Additionally, the MP treatment was found to significantly reduce the rhizosphere soil bacterial diversity and richness, including the Shannon, Chao1, observed species, and dominance indices (P < 0.05). Interestingly, the inoculation treatment also reduced microbial diversity, though the microbial diversity after treatment was similar to that of the control community structure, indicating its regulating effect on the soil microbial community. The abundance of Domibacillus, Pedosphaeraceae, and Enterococcus decreased due to the MP treatment, whereas Achromobacter, Massilia, Ralstonia, and Nitrosospira increased (P < 0.05). Furthermore, functional prediction indicated that MP treatment resulted in the enrichment of microbial functions, such as an AraC-type DNA-binding domain, etc. The microbial communities exposed to different sizes and concentrations of MPs had their own unique functions in response to the effects of the MPs. This study provided novel insights into the effects of different particle sizes and concentrations of MPs on the rhizosphere microbial community and agronomic traits of highland barley. It could be used to improve the understanding of the impact of MPs on the rhizosphere soil microecology and enhance bioremediation of MPs.

Differences in the microbiome of the small intestine of Leghorn lines divergently selected for antibody titer to sheep erythrocytes suggest roles for commensals in host humoral response

For forty generations, two lines of White Leghorn chickens have been selected for high (HAS) or low (LAS) antibody response to a low dose injection of sheep red blood cells (SRBCs). Their gut is home to billons of microorganisms and the largest number of immune cells in the body; therefore, the objective of this experiment was to gain understanding of the ways the microbiome may influence the differential antibody response observed in these lines. We achieved this by characterizing the small intestinal microbiome of HAS and LAS chickens, determining their functional microbiome profiles, and by using machine learning to identify microbes which best differentiate HAS from LAS and associating the abundance of those microbes with host gene expression. Microbiome sequencing revealed greater diversity in LAS but statistically higher abundance of several strains, particularly those of Lactobacillus, in HAS. Enrichment of microbial metabolites implicated in immune response such as lactic acid, short chain fatty acids, amino acids, and vitamins were different between HAS and LAS. The abundance of several microbial strains corresponds to enriched host gene expression pathways related to immune response. These data provide a compelling argument that the microbiome is both likely affected by host divergent genetic selection and that it exerts influence on host antibody response by various mechanisms.

Single-cell phenotyping of bacteria combined with deep sequencing for improved contextualization of microbiome analyses

Great effort was made to characterize the bacterial communities inhabiting the human body as a factor in disease, resulting in the realization that a wide spectrum of diseases is associated with an altered composition of the microbiome. However, the identification of disease-relevant bacteria has been hindered by the high cross-sectional diversity of individual microbiomes, and in most cases, it remains unclear whether the observed alterations are cause or consequence of disease. Hence, innovative analysis approaches are required that enable inquiries of the microbiome beyond mere taxonomic cataloging. This review highlights the utility of microbiota flow cytometry, a single-cell analysis platform to directly interrogate cellular interactions, cell conditions, and crosstalk with the host's immune system within the microbiome to take into consideration the role of microbes as critical interaction partners of the host and the spectrum of microbiome alterations, beyond compositional changes. In conjunction with advanced sequencing approaches it could reveal the genetic potential of target bacteria and advance our understanding of taxonomic diversity and gene usage in the context of the microenvironment. Single-cell bacterial phenotyping has the potential to change our perspective on the human microbiome and empower microbiome research for the development of microbiome-based therapy approaches and personalized medicine.

Effects of uranium mining on soil bacterial communities and functions in the Qinghai-Tibet plateau

The microecological effects of plateau uranium mining are still unknown. In this study, we used 16S rRNA high-throughput sequencing to analyze the impact of plateau uranium mining on the microbial diversity and community structure of tailings soil, tunnel soil, and soil at different depths in an open pit. The results showed that uranium mining significantly reduced soil microbial community richness and diversity indicators, including Chao1, Pielou evenness, and Shannon index (P < 0.05). Uranium mining activities significantly reduced the abundance of RB41, Vicinamidactaceae, and Nitrospira (P < 0.05). Interestingly, the abundance of Thiobacillus, Sphingomonas, and Sulfuriferula significantly increased in the soil samples from various environments and depths during uranium mining (P < 0.05). Beta diversity analysis found that uranium mining resulted in the differentiation of soil microbial communities. Functional enrichment analysis found that uranium mining resulted in the functional enrichment of DNA binding response regulator, DNA helicase, methyl-accepting chemotaxis protein, and Helicase conserved C-terminal domain, whereas cell wall synthesis, nonspecific serine/threonine protein kinase, RNA polymerase sigma-70 factor, and ATP binding cassette transporter were significantly affected by uranium mining (P < 0.05). In addition, we also found that different uranium mining environments and soil depths enriched diverse microbial populations and functions to cope with the environmental pressures that were elicited by uranium mining, including Gaiella, Gemmatimonas, Lysobacter, Pseudomonas, signal transformation histidine kinase, DNA-directed DNA polymerase, and iron complex outer membrane receptor protein functions (P < 0.05). The results have enhanced our understanding of the impact of uranium mining on plateau soil microecological stability and the mechanism of microbial response to uranium mining activities for the first time and aided us in screening microbial strains that can promote the environmental remediation of uranium mining in plateaus.

Understanding the bacterial community structure associated with the Eichhornia crassipes rootzone

BACKGROUND

Plant microbiome acts as an interface between plants and their environment, aiding in the functioning of the ecosystem, such as protection against abiotic and biotic stress along with improving nutrient uptake. The rhizosphere is an essential interface for the interaction between plants and microbes and plays a substantial part in the removal as well as uptake of heavy metals and antibiotics from contaminated locations. Eichhornia crassipes is a promising plant that contains a rich community of microbes in its rhizosphere. Microorganism's association with plants embodies a crucial pathway via which humans can also be exposed to antibiotic-resistant genes and bacteria.

METHODS AND RESULTS

In our earlier study enhanced removal of ciprofloxacin was observed by plant growth-promoting Microbacterium sp. WHC1 in the presence of E. crassipes root exudates. Therefore, the V3-V4, hypervariable region of the 16 S rRNA gene was studied to assess the bacterial diversity and functional profiles of the microbiota associated with plant roots. Using the QIIME software program, 16 S rRNA data from the Next Generation Sequencing (NGS) platform was examined. Alpha diversity including Chao1, Observed Shannon, and Simpson index denote significantly higher bacterial diversity. Proteobacteria (79%) was the most abundant phylum which was present in the root samples followed by Firmicutes (8%) and Cyanobacteria (8%). Sulfuricurvum (36%) is the most abundant genus belonging to the family Helicobacteraceae and the species kujiense in the genus Sulfuricurvum is the most abundant species present in the root sample. Also, the bacterial communities in the rhizoplane of Eichhornia crassipes harbor the genes conferring resistance to beta-lactams, tetracycline, fluoroquinolones, and penams.

CONCLUSION

Metagenomic studies on the E. crassipes microbiome showed that the bacterial communities constituting the root exudates of the Eichhornia aid them to survive in a polluted environment.

Dynamic Gut Microbiota of Apolygus lucorum Across Different Life Stages Reveals Potential Pathogenic Bacteria for Facilitating the Pest Management

Insect's gut microbiota has diverse effects on their fitness, and a comprehensive understanding of gut microbiota functions requires analyzing its diversity. Apolygus lucorum is a highly destructive pest that threatens many economically important crops in China. This study investigated the gut microbiota of A. lucorum across its life cycle using both culture-dependent and culture-independent methods. A total of 87 gut bacterial isolates were identified, belonging to 4 phyla, 27 families, and 45 genera, while Miseq sequencing detected 91 amplicon sequence variants (ASVs) assigned to 5 phyla, 28 families, and 39 genera. Proteobacteria and Firmicutes were the predominant phyla, with Staphylococcus and Serratia as the major genera. There were significant differences in the relative abundance of these genera between the nymph and adult stages. Staphylococcus was significantly more abundant in nymphs than it in adults, while Serratia was significantly more abundant in sexually mature adults than in other developmental stages. Notably, Serratia is a common opportunistic pathogen in many insects. Injecting the gut-dominant isolate Serratia marcescens verified its high pathogenicity. Additionally, immune indicators of the bug at different developmental stages supported the hypothesis that Serratia is a pathogen of A. lucorum. This study provides a foundation for understanding the role of gut bacteria in the life history of A. lucorum and developing new pest control strategies based on microbes.

Shrimp microbiome and immune development in the early life stages

With its contribution to nutrition, development, and disease resistance, gut microbiome has been recognized as a crucial component of the animal's health and well-being. Microbiome in the gastrointestinal tract constantly interacts with the host animal's immune systems as part of the normal function of the intestines. Interactions between the microbiome and the immune system are complex and dynamic, with the microbiome shaping immune development and function. In contrast, the immune system modulates the composition and activity of the microbiome. In shrimp, as with all other aquatic animals, the interaction between the microbiome and the animals occurs at the early developmental stages. This early interaction is likely essential to the development of immune responses of the animal as well as many key physiological developments that further contribute to the health of shrimp. This review provides background knowledge on the early developmental stage of shrimp and its microbiome, examines the interaction between the microbiome and the immune system in the early life stage of shrimp, and discusses potential pitfalls and challenges associated with microbiome research. Understanding the interaction between the microbiome and shrimp immune system at this crucial developmental stage could have the potential to aid in the establishment of a healthy microbiome, improve shrimp survival, and provide ways to shape the microbiome with feed supplements or other strategies.

The difference of intestinal microbiota composition between Lantang and Landrace newborn piglets

BACKGROUND

The early development of intestinal microbiota plays a fundamental role in host health and development. To investigate the difference in the intestinal microbial composition between Lantang and Landrace newborn piglets, we amplified and sequenced the V3-V4 region of 16 S rRNA gene in jejunal microbiota of Lantang and landrace newborn.

RESULTS

The findings revealed that the dominant phyla in the jejunum of Lantang piglets were Firmicutes, Actinobacteria and Bacteroidetes, while the dominant phyla of Landrace is Proteobacteria and Fusobacteria. Specifically, Corynebacterium_1, Lactobacillus, Rothia, Granulicatella, Corynebacteriales_unclassified, Corynebacterium, Globicatella and Actinomycetales_unclassified were found to be the dominant genera of Lantang group, while Clostridium_sensu_stricto_1, Escherichia-Shigella, Actinobacillus and Bifidobacterium were the dominant genera of Landrace. Based on the functional prediction of bacteria, we found that bacterial communities from Lantang samples had a significantly greater abundance pathways of fatty acid synthesis, protein synthesis, DNA replication, recombination, repair and material transport across membranes, while the carrier protein of pathogenic bacteria was more abundant in Landrace samples.

CONCLUSIONS

Overall, there was a tremendous difference in the early intestinal flora composition between Landang and Landrace piglets, which was related to the breed characteristics and may be one of the reasons affecting the growth characteristics. However, more further extensive studies should be included to reveal the underlying relationship between early intestinal flora composition in different breeds and pig growth characteristics.

Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches

AIMS

The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota.

METHODS AND RESULTS

Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively.

CONCLUSIONS

A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential.

IMPACT STATEMENT

The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.

Deciphering the functional diversity of the gut microbiota of the black soldier fly (Hermetia illucens): recent advances and future challenges

Bioconversion using insects is a promising strategy to convert organic waste (catering leftovers, harvest waste, food processing byproducts, etc.) into biomass that can be used for multiple applications, turned into high added-value products, and address environmental, societal and economic concerns. Due to its ability to feed on a tremendous variety of organic wastes, the black soldier fly (Hermetia illucens) has recently emerged as a promising insect for bioconversion of organic wastes on an industrial scale. A growing number of studies have highlighted the pivotal role of the gut microbiota in the performance and health of this insect species. This review aims to provide a critical overview of current knowledge regarding the functional diversity of the gut microbiota of H. illucens, highlighting its importance for bioconversion, food safety and the development of new biotechnological tools. After providing an overview of the different strategies that have been used to outline the microbial communities of H. illucens, we discuss the diversity of these gut microbes and the beneficial services they can provide to their insect host. Emphasis is placed on technical strategies and aspects of host biology that require special attention in the near future of research. We also argue that the singular digestive capabilities and complex gut microbiota of H. illucens make this insect species a valuable model for addressing fundamental questions regarding the interactions that insects have evolved with microorganisms. By proposing new avenues of research, this review aims to stimulate research on the microbiota of a promising insect to address the challenges of bioconversion, but also fundamental questions regarding bacterial symbiosis in insects.

16S rDNA Sequencing-Based Insights into the Bacterial Community Structure and Function in Co-Existing Soil and Coal Gangue

Coal gangue is a solid waste emitted during coal production. Coal gangue is deployed adjacent to mining land and has characteristics similar to those of the soils of these areas. Coal gangue-soil ecosystems provide habitats for a rich and active bacterial community. However, co-existence networks and the functionality of soil and coal gangue bacterial communities have not been studied. Here, we performed Illumina MiSeq high-throughput sequencing, symbiotic network and statistical analyses, and microbial phenotype prediction to study the microbial community in coal gangue and soil samples from Shanxi Province, China. In general, the structural difference between the bacterial communities in coal gangue and soil was large, indicating that interactions between soil and coal gangue are limited but not absent. The bacterial community exhibited a significant symbiosis network in soil and coal gangue. The co-occurrence network was primarily formed by Proteobacteria, Firmicutes, and Actinobacteria. In addition, BugBase microbiome phenotype predictions and PICRUSt bacterial functional potential predictions showed that transcription regulators represented the highest functional category of symbiotic bacteria in soil and coal gangue. Proteobacteria played an important role in various processes such as mobile element pathogenicity, oxidative stress tolerance, and biofilm formation. In general, this work provides a theoretical basis and data support for the in situ remediation of acidified coal gangue hills based on microbiological methods.

Microbial genome (Illumina MiSeq) sequencing of drinking water treatment residuals to evaluate compatibility with environmental applications

The clarification of drinking water leads to the production of large quantities of water treatment residuals (WTRs). DNA was extracted from six WTR samples collected from water treatment plants within the UK to compare their bacterial communities and examine whether factors such as coagulant usage (aluminium versus iron salt), the type of water source (reservoir or river), or leachable chemical composition influence these communities. Bacterial 16S variable region 4 (V4) was amplified and sequenced using Illumina MiSeq sequencing. The most abundant phyla in WTR samples were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes, collectively representing 92.77-97.8% of the total bacterial sequences. Statistical analysis of microbial profiles indicated that water source played a significant role in microbial community structure, diversity, and richness, however coagulant type did not. PERMANOVA analysis showed that no single chemical variable (pH, organic matter, or extractable element concentration) influenced microbial composition significantly; however, canonical correspondence analysis of WTR microbiomes yielded a model using all these variables that could be used to explain variations in microbial community structures of WTRs (p < 0.05). No common, potentially toxic cyanobacteria, or related pathogens of concern were found. Analysis with PICRUSt showed that WTRs all had similar predicted microbial functional profiles. Overall, the results indicate that WTRs analysed in this study are unlikely to pose any threat to soil microbial community structure when applied to land as a soil conditioner or enhancer and may help to enhance the soil microbial community.

A preliminary study of the salivary microbiota of young male subjects before, during, and after acute high-altitude exposure

Background

The microbial community structure in saliva differs at different altitudes. However, the impact of acute high-altitude exposure on the oral microbiota is unclear. This study explored the impact of acute high-altitude exposure on the salivary microbiome to establish a foundation for the future prevention of oral diseases. Methods. Unstimulated whole saliva samples were collected from 12 male subjects at the following three time points: one day before entering high altitude (an altitude of 350 m, pre-altitude group), seven days after arrival at high altitude (an altitude of 4,500 m, altitude group) and seven days after returning to low altitude (an altitude of 350 m, post-altitude group). Thus, a total of 36 saliva samples were obtained. 16S rRNA V3-V4 region amplicon sequencing was used to analyze the diversity and structure of the salivary microbial communities, and a network analysis was employed to investigate the relationships among salivary microorganisms. The function of these microorganisms was predicted with a Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.

Results

In total, there were 756 operational taxonomic units (OTUs) identified, with 541, 613, and 615 OTUs identified in the pre-altitude, altitude, and post-altitude groups, respectively. Acute high-altitude exposure decreased the diversity of the salivary microbiome. Prior to acute high-altitude exposure, the microbiome mainly consisted of Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria. After altitude exposure, the relative abundance of Streptococcus and Veillonella increased, and the relative abundance of Prevotella, Porphyromonas, and Alloprevotella decreased. The relationship among the salivary microorganisms was also affected by acute high-altitude exposure. The relative abundance of carbohydrate metabolism gene functions was upregulated, while the relative abundance of coenzyme and vitamin metabolism gene functions was downregulated.

Conclusion

Rapid high-altitude exposure decreased the biodiversity of the salivary microbiome, changing the community structure, symbiotic relationships among species, and abundance of functional genes. This suggests that the stress of acute high-altitude exposure influenced the stability of the salivary microbiome.

Biochemical Recurrence in Prostate Cancer Is Associated with the Composition of Lactobacillus: Microbiome Analysis of Prostatic Tissue

Many human pathologies, such as malignancy, are linked with specific bacteria and changes in the constituents of the microbiome. In order to examine the association between an imbalance of bacteria and prostate carcinoma, a comparison of the microbiomes present in patients with biochemical recurrence (BCR) or NO BCR (NBCR) was performed. Additionally, 16S rRNA-based next-generation sequencing was applied to identify the bacterial profiles within these tumors in terms of the bacteria and operational genes present. The percentage average taxonomic composition between the taxa indicated no difference between BCR and NBCR. In addition, alpha and beta diversity indices presented no distinction between the cohorts in any statistical method. However, taxonomic biomarker discovery indicated a relatively higher population of Lactobacillus in the NBCR group, and this finding was supported by PCR data. Along with that, differences in the operational activity of the bacterial genes were also determined. It is proposed that the biochemical recurrence was linked to the quantity of Lactobacillus present. The aim of this study was to investigate the microbiome involved in prostate carcinoma and the potential association between them.

Exploring the characteristics of gut microbiome in patients of Southern Fujian with hypocitraturia urolithiasis and constructing clinical diagnostic models

PURPOSE

Hypocitraturia is an important cause of urolithiasis. Exploring the characteristics of the gut microbiome (GMB) of hypocitriuria urolithiasis (HCU) patients can provide new ideas for the treatment and prevention of urolithiasis.

METHODS

The 24 h urinary citric acid excretion of 19 urolithiasis patients was measured, and patients were divided into the HCU group and the normal citrate urolithiasis (NCU) group. The 16 s ribosomal RNA (rRNA) was used to detect GMB composition differences and construct operational taxonomic units (OTUs) coexistence networks. The key bacterial community was determined by Lefse analysis, Metastats analysis and RandomForest analysis. Redundancy analysis (RDA) and Pearson correlation analysis visualized the correlation between key OTUs and clinical features and then established the disease diagnosis model of microbial-clinical indicators. Finally, PICRUSt2 was used to explore the metabolic pathway of related GMB in HCU patients.

RESULTS

The alpha diversity of GMB in HCU group was increased and Beta diversity analysis suggested significant differences between HCU and NCU groups, which was related to renal function damage and urinary tract infection. Ruminococcaceae_ge and Turicibacter are the characteristic bacterial groups of HCU. Correlation analysis showed that the characteristic bacterial groups were significantly associated with various clinical features. Based on this, the diagnostic models of microbiome-clinical indicators in HCU patients were constructed with the areas under the curve (AUC) of 0.923 and 0.897, respectively. Genetic and metabolic processes of HCU are affected by changes in GMB abundance.

CONCLUSION

GMB disorder may be involved in the occurrence and clinical characteristics of HCU by influencing genetic and metabolic pathways. The new microbiome-clinical indicator diagnostic model is effective.

Microbiome in paired root apices and periapical lesions and its association with clinical signs in persistent apical periodontitis using next-generation sequencing

AIM

To assess and compare the microbiome of paired root apices and periapical lesions from cases with failed endodontic treatment and to associate the microbiome and bacterial metabolic pathways in both sites with asymptomatic apical periodontitis (AAP) and symptomatic apical periodontitis (SAP), using next-generation sequencing (NGS).

METHODOLOGY

Matched root apices and periapical lesions of patients with failed root canal treatments were surgically extracted. Specimens were cryopulverized, bacterial DNA was extracted and the V3-V4 hypervariable regions of the 16 S rRNA gene were amplified and sequenced using the Illumina Miseq platform. Diversity and community composition were studied in the paired samples, as well as in AAP and SAP cases. Diversity indices were compared in each case by means of the Wilcoxon matched-pairs signed rank and Mann-Whitney U tests. Differences in the community composition were explored with multivariate statistical analysis and Linear discriminant analysis Effect Size (LEfSe). Bacterial functional study was performed through the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis.

RESULTS

Twenty-one paired apices and lesions were successfully sequenced and analysed, identifying a total of 21 phyla and 600 genera. A higher alpha-diversity was observed in the periapical lesions, although no global differences in the community composition between the two sites were found (p = .87), the most prevalent genera being Fusobacterium, Porphyromonas and Streptococcus. Prevotella, Clostridiales_vadinBB60_group, Bosea, Phreatobacter, Afipia and Xanthobacteriaceae_unclassified were enriched in SAP samples, while Pseudopropionibacterium, Campylobacter and Peptoniphilus were significantly more abundant in AAP cases (p < .05). Metabolic pathways involved in the amino acid metabolism or degradation and flagellum assembly were more abundant in SAP samples, whereas glucose metabolism-related pathways were associated with AAP.

CONCLUSIONS

The bacterial community composition was similar in the apices and periapical lesions. The microbiome was different in AAP and SAP samples, gram-negative bacteria showing higher relative abundances in SAP cases. An association was observed between amino acid degradation and flagellum assembly pathways, and the development of tenderness to percussion or palpation.

Prediction and validation of microbial community function from normal pulp to pulpitis caused by deep dentinal caries

INTRODUCTION

Microbial function changes may be responsible for dental pulp transformation from normal to diseased. However, studies on the prediction and verification of the function of the microbial community in the deep dentine and pulp of caries-induced pulpitis are lacking.

METHODS

This study included 171 cases of deep dentinal caries divided into normal pulp (NP), reversible pulpitis (RP), and irreversible pulpitis (IRP). In Experiment I, the microbial community composition was identified in 111 samples using 16S ribosomal DNA. Function prediction was performed through phylogenetic investigation of communities by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States prediction and qPCR. In Experiment II, different microbiome functions were confirmed in 60 samples using liquid chromatography-tandem mass spectrometry.

RESULTS

In Experiment I, microbial abundance significantly differed in the IRP group compared to the other two groups. The RP and NP groups had the same microbiome composition, but the predicted functional difference between the RP and NP groups pertained to membrane transport (p < .010). The predicted functional difference between the IRP and NP groups pertained to amino-acid, co-factor, and vitamin metabolism (p < .010). In Experiment II, Kyoto Encyclopedia of Genes and Genomes functional annotation revealed that the differential metabolites between the RP and NP groups did not participate in membrane transport; however, the differential metabolites between the IRP and NP groups participated in amino-acid metabolism.

CONCLUSIONS

The near-pulp microbiome in RP and NP with deep dentinal caries had the same differential function. However, amino acid metabolism in near the pulp microbial community differed between IRP and NP with deep dentinal caries.

Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes

BACKGROUND

Diabetes mellitus (DM) is a major risk factor for tuberculosis (TB). Evidence has linked the DM-related dysbiosis of gut microbiota to modifiable host immunity to Mycobacterium tuberculosis infection. However, the crosslinks between gut microbiota composition and immunological effects on the development of latent TB infection (LTBI) in DM patients remain uncertain.

METHODS

We prospectively obtained stool, blood samples, and medical records from 130 patients with poorly-controlled DM (pDM), defined as ever having an HbA1c > 9.0% within previous 1 year. Among them, 43 had LTBI, as determined by QuantiFERON-TB Gold in-Tube assay. The differences in the taxonomic diversity of gut microbiota between LTBI and non-LTBI groups were investigated using 16S ribosomal RNA sequencing, and a predictive algorithm was established using a random forest model. Serum cytokine levels were measured to determine their correlations with gut microbiota.

RESULTS

Compared with non-LTBI group, the microbiota in LTBI group displayed a similar alpha-diversity but different beta-diversity, featuring decrease of Prevotella_9, Streptococcus, and Actinomyces and increase of Bacteroides, Alistipes, and Blautia at the genus level. The accuracy was 0.872 for the LTBI prediction model using the aforementioned 6 microbiome-based biomarkers. Compared with the non-LTBI group, the LTBI group had a significantly lower serum levels of IL-17F (p = 0.025) and TNF-α (p = 0.038), which were correlated with the abundance of the aforementioned 6 taxa.

CONCLUSIONS

The study results suggest that gut microbiome composition maybe associated with host immunity relevant to TB status, and gut microbial signature might be helpful for the diagnosis of LTBI.

Composition and factors influencing community structure of lactic acid bacterial in dairy products from Nyingchi Prefecture of Tibet

This study investigated the community composition of lactic acid bacteria (LAB) from yaks' milk (YM) Tibetan yellow cattle milk (TM) and their fermented products from different counties in the Nyingchi Prefecture, Tibet using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. Sequencing revealed 26 genera and 94 species from 71 dairy samples; amongst these Lactobacillus delbrueckii (36.17%), Streptococcus thermophilus (19.46%) and Lactococcus lactis (18.33%) were the predominant species. This study also identified the main factors influencing LAB community composition by comparing amongst samples from different locations, from different milk types, and from different altitudes. The LAB communities in YM and TM were more diverse than in fermented yaks' milk (FYM) and fermented Tibetan yellow cattle milk (FTM) samples. Similarly, whether milk was fermented or not accounted for differences in LAB species composition while altitude of the dairy products had very little effect. Milk source and production process were the most likely causes of drastic shifts in microbial community composition. In addition, fermented dairy products were enriched in genes responsible for secondary metabolic pathways that were potentially beneficial for health. Comprehensive descriptions of the microbiota in different dairy products from the Nyingchi Prefecture, Tibet might help elucidate evolutionary and functional relationships amongst bacterial communities in these products.

Carapace microbiota in American lobsters (Homarus americanus) associated with epizootic shell disease and the green gland

Epizootic Shell Disease (ESD) has posed a great threat, both ecologically and economically, to the American lobster population of Long Island Sound since its emergence in the late 1990s. Because of the polymicrobial nature of carapace infections, causative agents for ESD remain unclear. In this study, we aimed to identify carapace microbiota associated with ESD and its potential impact on the microbiota of internal organs (green gland, hepatopancreas, intestine, and testis) using high-throughput 16S rRNA gene sequencing. We found that lobsters with ESD harbored specific carapace microbiota characterized by high abundance of Aquimarina, which was significantly different from healthy lobsters. PICRUSt analysis showed that metabolic pathways such as amino acid metabolism were enriched in the carapace microbiota of lobsters with ESD. Aquimarina, Halocynthiibacter, and Tenacibaculum were identified as core carapace bacteria associated with ESD. Particularly, Aquimarina and Halocynthiibacter were detected in the green gland, hepatopancreas, and testis of lobsters with ESD, but were absent from all internal organs tested in healthy lobsters. Hierarchical clustering analysis revealed that the carapace microbiota of lobsters with ESD was closely related to the green gland microbiota, whereas the carapace microbiota of healthy lobsters was more similar to the testis microbiota. Taken together, our findings suggest that ESD is associated with alterations in the structure and function of carapace microbiota, which may facilitate the invasion of bacteria into the green gland.

Efficacy of Yougui pill combined with Buzhong Yiqi decoction in alleviating the sexual dysfunction in female rats through modulation of the gut microbiota

CONTEXT

Yougui pill combined with Buzhong Yiqi decoction (YPBYD) is used to relieve sexual dysfunction in clinical practice.

OBJECTIVE

To investigate changes in microbial composition caused by sexual dysfunction and identify dominant bacteria related to YPBYD treatment.

MATERIALS AND METHODS

Female Sprague-Dawley rats were randomly divided into four groups (n = 6): one group underwent Sham operation (Sham group), while three groups underwent ovariectomy (one model and two treatment groups). The ovariectomized (OVX) rats received oestradiol benzoate (250 µg/kg/week) or YPBYD (3.6 mL/d) via oral gavage for 4 weeks. Vaginal smear assay was performed; the serum levels of cyclic adenosine monophosphate (cAMP) and oestradiol (E2) were measured, followed by collection of stool samples for 16S rRNA sequencing.

RESULTS

After YPBYD treatment, the levels of E2 and cAMP in OVX rats significantly increased (E2: from 20.45 ± 1.60 ng/L to 24.38 ± 1.70 ng/L; cAMP: from 261.41 ± 9.21 pg/mL to 373.75 ± 17.37 pg/mL). OVX treatment decreased diversity of gut microbiota and YPBYD treatment restored gut microbiota composition. Compared with Sham group, the abundance of Romboutsia significantly increased, while those of Proteobacteria and Staphylococcus markedly decreased in OVX group (all p < 0.05); meanwhile, the abundance of these microbes showed an opposite trend after YPBYD treatment. These microbiotas were involved in tyrosine and tryptophan biosynthesis and fatty acid metabolism.

DISCUSSION AND CONCLUSIONS

These findings are the first to indicate YPBYD can alleviate female sexual dysfunction by modulating gut microbiota in OVX rats, which will help enhance the understanding on potential mechanism of YPBYD against sexual dysfunction.

Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas

Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.