Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

16S rRNA Sequencing Reveals Alterations of Gut Bacteria in Hirschsprung-Associated Enterocolitis

Hirschsprung-associated enterocolitis (HAEC) stands as most common and serious complication of Hirschsprung's disease. Variations in the microbiota composition may account for the differences observed between HAEC and healthy individuals, offering crucial insights into the disease's pathogenesis. Here, we performed a study to changes in the gut microbiome using 16sRNA amplicon sequencing in a cohort of HAEC patients ( n  = 16) and healthy controls ( n  = 14). Our result revealed a significant disparity in beta diversity between the two groups. Following correction for false discovery rate, a rank-sum test at the genus level indicated a notable decrease in the relative abundance of Bifidobacterium , Lactobacillus , and Veillonella , whereas the Enterococcus genus exhibited a substantial increase in HAEC, a finding further supported by additional linear discriminant analysis effect size analysis. Functional analysis showed that putative transport and catabolism, digestive system, and metabolism of cofactors and vitamins were proved to be some abundant KOs (Kyoto Encyclopedia of Genes and Genomes [KEGG] orthologs) in healthy group, whereas infectious disease, membrane transport, and carbohydrate metabolism were the three KOs with the higher abundance in the HAEC group. Our data increased our insight into the HAEC, which may shed further light on HAEC pathogenesis. Our study firstly demonstrated the difference between fecal microbiota of HAEC patients and healthy individuals, which made a step forward in the understanding of the pathophysiology of HAEC.

Disturbance of the human gut microbiota in patients with Myotonic Dystrophy type 1

Myotonic dystrophy type 1 (DM1) is a rare autosomal dominant genetic disorder. Although DM1 is primarily characterized by progressive muscular weakness, it exhibits many multisystemic manifestations, such as cognitive deficits, cardiac conduction abnormalities, and cataracts, as well as endocrine and reproductive issues. Additionally, the gastrointestinal (GI) tract is frequently affected, encompassing the entire digestive tract. However, the underlying causes of these GI symptoms remain uncertain, whether it is biomechanical problems of the intestine, involvement of bacterial communities, or both. The primary objective of this study is to investigate the structural changes in the gut microbiome of DM1 patients. To achieve this purpose, 35 patients with DM1 were recruited from the DM-Scope registry of the neuromuscular clinic in the Saguenay-Lac-St-Jean region of the province of Québec, Canada. Stool samples from these 35 patients, including 15 paired samples with family members living with them as controls, were collected. Subsequently, these samples were sequenced by 16S MiSeq and were analyzed with DADA2 to generate taxonomic signatures. Our analysis revealed that the DM1 status correlated with changes in gut bacterial community. Notably, there were differences in the relative abundance of Bacteroidota, Euryarchaeota, Fusobacteriota, and Cyanobacteria Phyla compared to healthy controls. However, no significant shift in gut microbiome community structure was observed between DM1 phenotypes. These findings provide valuable insights into how the gut bacterial community, in conjunction with biomechanical factors, could potentially influence the gastrointestinal tract of DM1 patients.

Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma

Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). Fecal specimens were obtained from 16 healthy controls, 33 patients with viral-HCC (17 and 16 cases with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, respectively), and 18 patients with NBNC-HCC. Compositions of fecal microbiota were assessed by 16S rRNA sequencing. Bioinformatic analysis was performed by the DADA2 pipeline in the R program. Significantly different genera from the top 50 relative abundance were used to classify between subgroups of HCC by the Random Forest algorithm. Our data demonstrated that the HCC group had a significantly decreased alpha-diversity and changed microbial composition in comparison with healthy controls. Within the top 50 relative abundance, there were 11 genera including Faecalibacterium, Agathobacter, and Coprococcus that were significantly enhanced in Viral-HCC, while 5 genera such as Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium were enhanced in NBNC-HCC. Compared to Viral-HCC, the NBNC-HCC subgroup significantly reduced various short-chain fatty acid-producing bacteria, as well as declined fecal butyrate but elevated plasma surrogate markers of microbial translocation. Based on the machine learning algorithm, a high diagnostic accuracy to classify HCC subgroups was achieved with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.94. Collectively, these data revealed that gut dysbiosis was distinct according to etiological factors of HCC, which might play an essential role in hepatocarcinogenesis. These findings underscore the possible use of a gut microbiota signature for the diagnosis and therapeutic approaches regarding different subgroups of HCC. KEY POINTS: • Gut dysbiosis is connected to hepatocarcinogenesis and can be used as a novel biomarker. • Gut microbiota composition is significantly altered in different etiological factors of HCC. • Microbiota-based signature can accurately distinguish between Viral-HCC and NBNC-HCC.

Role of folic acid in regulating gut microbiota and short-chain fatty acids based on an in vitro fermentation model

Folic acid deficiency is common worldwide and is linked to an imbalance in gut microbiota. However, based on model animals used to study the utilization of folic acid by gut microbes, there are challenges of reproducibility and individual differences. In this study, an in vitro fecal slurry culture model of folic acid deficiency was established to investigate the effects of supplementation with 5-methyltetrahydrofolate (MTHF) and non-reduced folic acid (FA) on the modulation of gut microbiota. 16S rRNA sequencing results revealed that both FA (29.7%) and MTHF (27.9%) supplementation significantly reduced the relative abundance of Bacteroidetes compared with control case (34.3%). MTHF supplementation significantly improved the relative abundance of Firmicutes by 4.49%. Notably, compared with the control case, FA and MTHF supplementation promoted an increase in fecal levels of Lactobacillus, Bifidobacterium, and Pediococcus. Short-chain fatty acid (SCFA) analysis showed that folic acid supplementation decreased acetate levels and increased fermentative production of isobutyric acid. The in vitro fecal slurry culture model developed in this study can be utilized as a model of folic acid deficiency in humans to study the gut microbiota and demonstrate that exogenous folic acid affects the composition of the gut microbiota and the level of SCFAs. KEY POINTS: • Establishment of folic acid deficiency in an in vitro culture model. • Folic acid supplementation regulates intestinal microbes and SCFAs. • Connections between microbes and SCFAs after adding folic acid are built.

Biotransformation characteristics of urate-lowering probiotic fermented apple juice and potential regulatory mechanisms for ameliorating hyperuricemia via mediating gut microbiota and metabolic pathways

Hyperuricemia has evolved into a global public health concern, and applying probiotics fermented apple juice holds promise for alleviating this condition. This study aimed to investigate the biotransformation and metabolic features of urate-lowering probiotics sequentially fermented dealcoholized apple juice (PSFA), and assess its ameliorative effects and potential mechanisms on hyperuricemia mice. Results showed that CICC 6074 and 20,292 possessed excellent purine, nucleotide and nucleoside degradation and acid and bile salt resistance; sequential fermentation decreased the fructose in apple juice, and viable counts reached 3.76 × 108 CFU/mL. Histopathological analysis showed that PSFA ameliorated kidney damage in hyperuricemia mice. Furthermore, PSFA significantly reduced Urea, Creatinine and Uric acid levels in hyperuricemia mice; and inhibited xanthine oxidase activity and the expression of pro-inflammatory factors. Importantly, PSFA reversed gut microbiota dysbiosis and raised the abundance of beneficial bacteria (Lactobacillush, Faecalibaculum and Lachnospiraceae_NK4A136_group). KEGG and COG functional prediction results revealed that the potential mechanism of PSFA to ameliorate hyperuricemia may be lipid metabolism and glycolysis pathways.

Microbiota diversity of three Brazilian native fishes during ice and frozen storage

This study aimed to assess the bacterial microbiota involved in the spoilage of pacu (Piaractus mesopotamics), patinga (female Piaractus mesopotamics x male Piaractus brachypomus), and tambacu (female Colossoma macropomum × male Piaractus mesopotamics) during ice and frozen storage. Changes in the microbiota of three fish species (N = 22) during storage were studied through 16S rRNA amplicon-based sequencing and correlated with volatile organic compounds (VOCs) and metabolites assessed by nuclear magnetic resonance (NMR). Storage conditions (time and temperature) affected the microbiota diversity in all fish samples. Fish microbiota comprised mainly of Pseudomonas sp., Brochothrix sp., Acinetobacter sp., Bacillus sp., Lactiplantibacillus sp., Kocuria sp., and Enterococcus sp. The relative abundance of Kocuria, P. fragi, L. plantarum, Enterococcus, and Acinetobacter was positively correlated with the metabolic pathways of ether lipid metabolism while B. thermosphacta and P. fragi were correlated with metabolic pathways involved in amino acid metabolism. P. fragi was the most prevalent spoilage bacteria in both storage conditions (ice and frozen), followed by B. thermosphacta. Moreover, the relative abundance of identified Bacillus strains in fish samples stored in ice was positively correlated with the production of VOCs (1-hexanol, nonanal, octenol, and 2-ethyl-1-hexanol) associated with off-flavors. 1H NMR analysis confirmed that amino acids, acetic acid, and ATP degradation products increase over (ice) storage, and therefore considered chemical spoilage index of fish fillets.

The influence of vermicompost on atrazine microbial degradation performance and pathway in black soil, Northeast China

The atrazine (ATR) is extensively used in dryland crops like corn and sorghum in black soil region of Northeast China, posing ecological risks due to toxic metabolites. Vermicompost are known for soil organic pollution remediation but their role in pesticide degradation in black soil remains understudied. The influence of vermicompost on the microbial degradation pathway of atrazine was assessed in this study. Although vermicompost didn't significantly boost atrazine removal, they notably aided in primary metabolite degradation, hydroxyatrazine (HYA), deisopropylatrazine (DIA), and deethylatrazine (DEA), reducing their content by 38.67 %. They also altered the soil microbial community structure, favoring atrazine-degrading bacteria like Proteobacteria, Firmicutes, and Actinobacteria. Five secondary degradation products were identified in vermicompost treatments. Atrazine degradation occurred via dechlorination, dealkylation, and deamination pathways mainly by Nocardioidacea, Streptomycetaceae, Bacillaceae, Sphingomonadaceae, Comamonadaceae and Nitrososphaeraceae. pH and available nitrogen (AN) influenced microbial community structure and atrazine degradation, correlating with vermicompost application rates. Future black soil remediation should optimize application rates based on atrazine content and soil properties.

Differential contribution of microbial and plant-derived organic matter to soil organic carbon sequestration over two decades of natural revegetation and cropping

Both natural revegetation and cropping have great impact on long-term soil carbon (C) sequestration, yet the differences in their underlying mechanisms remain unclear. In this study, we investigated trends in soil organic C (SOC) accumulation during natural revegetation (VR) and cropping processes over 24 years, and explored the contributions of microbial necromass and plant-derived C to SOC formation and their primary controls. Over the course of 24 years of land use/cover change (LUCC) from 1995, SOC content exhibited a more substantial increase in VR (0.31 g kg-1 a-1) than in cropland (0.14 g kg-1 a-1) during Stage II (>10 y after LUCC), and recalcitrant organic carbon explained more of the SOC variation than easily oxidizable carbon. The higher SOC content in VR was attributed to a greater contribution of plant-derived C (14-28 %) than that in cropland (3-11 %) to SOC and a consistently lower ratio of cinnamyl (C)- to vanillyl (V)-type phenols in VR across all the assessed years. Although there were higher proportion of microbial necromass of SOC (41-84 %) in cropland than in VR, the differences were not significant. The dominant bacterial phylum of Chloroflexi and soil nitrogen content were the primary biotic and abiotic factors regulating microbial-derived and plant-derived C in both cropland and VR. However, soil phosphorus content was the main factor in cropland, while climatic factors such as mean annual precipitation were more important in VR. These results provided evidence that long-term natural revegetation enhanced SOC sequestration by greater contribution of plant-derived C to SOC formation compared to cropping. These findings underscore the synergistic contribution of vegetation and microorganisms to long-term SOC sequestration, offering insights into the different mechanisms of carbon formation during VR and cropping processes, and providing support for optimizing land management to achieve global carbon neutrality goals.

Pre-anoxic electro-stimulation enhanced simultaneous nitrification-denitrification in single-stage electrolysis-integrated sequencing batch biofilm reactor

Simultaneous nitrification-denitrification (SND) is a promising nitrogen removal process. However, total nitrogen (TN) removal is limited due to unsatisfactory denitrification. This study demonstrated that short-time (1 h) pre-anoxic electro-stimulation significantly enhanced SND efficiency in the aerobic phase by promoting the proliferation of mixotrophic and heterotrophic denitrifiers. SND and TN removal efficiencies at the optimal electric current (EC) (0.02 A) were 85.6 % and 93.9 %, which were 39.1 % and 17.2 % higher than control. Microbial community analysis indicated that the abundance of mixotrophic and heterotrophic denitrifiers significantly increased. H2 generated in the electro-stimulation process induced the proliferation of mixotrophic denitrifiers. The weak EC (0.02 A) promoted the activity and growth of heterotrophic denitrifiers by accelerating electron transfer. They concurrently mediated heterotrophic denitrification to enhance SND efficiency. PICRUSt2 analysis revealed that the abundance of denitrifying genes dramatically surged. This study provides new insights into applying electrolysis to achieve advanced SND while minimizing electricity consumption.

Sludge bound-EPS solubilization enhance CH4 bioconversion and membrane fouling mitigation in electrochemical anaerobic membrane bioreactor: Insights from continuous operation and interpretable machine learning algorithms

Bound extracellular polymeric substances (EPS) are complex, high-molecular-weight polymer mixtures that play a critical role in pore clogging, foulants adhesion, and fouling layer formation during membrane filtration, owing to their adhesive properties and gelation tendencies. In this study, a novel electrochemical anaerobic membrane bioreactor (EC-AnMBR) was constructed to investigate the effect of sludge bound-EPS solubilization on methane bioconversion and membrane fouling mitigation. During the 150-days' operation, the EC-AnMBR demonstrated remarkable performance, characterized by an exceptionally low fouling rate (transmembrane pressure (TMP) < 4.0 kPa) and high-quality effluent (COD removal > 98.2 %, protein removal > 97.7 %, and polysaccharide removal > 98.5 %). The highest methane productivity was up to 38.0 ± 3.1 mL/Lreactor/d at the applied voltage of 0.8 V with bound-EPS solubilization, 107.6 % higher than that of the control stage (18.3 ± 2.4 mL/Lreactor/d). Morphological and multiplex fluorescence labeling analyses revealed higher fluorescence intensities of proteins, polysaccharides, total cells and lipids on the surface of the fouling layer. In contrast, the interior exhibited increased compression density and reduced activity, likely attributable to compression effect. Under the synergistic influence of the electric field and bound-EPS solubilization, biomass characteristics exhibited a reduced propensity for membrane fouling. Furthermore, the bio-electrochemical regulation enhanced the electroactivity of microbial aggregates and enriched functional microorganisms, thereby promoting biofilm growth and direct interspecies electron transfer. Additionally, the potential hydrogenotrophic and methylotrophic methanogenesis pathways were enhanced at the cathode and anode surfaces, thereby increasing CH₄ productivity. The random forest-based machine learning model analyzed the nonlinear contributions of EPS characteristics on methane productivity and TMP values, achieving R² values of 0.879 and 0.848, respectively. Shapley additive explanations (SHAP) analysis indicated that S-EPSPS and S-EPSPN were the most critical factors affecting CH₄ productivity and membrane fouling, respectively. Partial dependence plot analysis further verified the marginal and interaction effects of different EPS layers on these outcomes. By combining continuous operation with interpretable machine learning algorithms, this study unveils the intricate impacts of EPS characteristics on methane productivity and membrane fouling behaviors, and provides new insights into sludge bound-EPS solubilization in EC-AnMBR.

Dietary Chlorella vulgaris supplementation modulates health, microbiota and the response to oxidative stress of Atlantic salmon

Microalgae are emerging as functional feed ingredients in aquaculture due to their immune-stimulating and stress-modulating properties. We investigated the potential of the microalgae Chlorella vulgaris as a feed supplement to improve the health and modulate microbiota and stress responses of Atlantic salmon. Triplicate groups of Atlantic salmon (~ 126 g) were reared in a recirculating aquaculture system (RAS) at 15 °C and received diets supplemented with 2% (CV2) or 14% (CV14) spray-dried C. vulgaris daily, 14% once weekly (CV14w), or a control diet (CD) for 8 weeks. Subsequently, all groups were exposed to an acute one-hour peracetic acid (CH3CO3H; PAA) treatment, a commonly used disinfectant in RAS. While CV14 increased feed conversion (FCR) significantly, feeding the diets CV2 and CV14w improved protein retention efficiency. CV14 significantly modulated beta-diversity in the intestinal digesta and mucosa, but this effect was already visible in fish fed CV2. Feeding CV14 and, to a lesser degree, CV2 increased the relative abundances of Paenarthrobacter and Trichococcus in the digesta and mucosa, which are able to metabolize complex carbohydrates. However, the same diets reduced the abundance of the lactic acid bacteria Lactobacillus and Weissella in the digesta and Floricoccus in the mucosa. Peracetic acid exposure induced systemic stress (increase in plasma glucose and cortisol) and a local immune response in the gill, with the most prominent upregulation of several immune- and stress-regulated genes (clra, cebpb, marco, tnfrsf14, ikba, c1ql2, drtp1) 18 h after exposure in fish fed the control diet. Fish receiving CV14 once a week showed a reduced transcriptional response to PAA exposure. Catalase protein abundance in the liver increased following exposure to PAA, while superoxide dismutase abundance in the gill and liver was increased in response to C. vulgaris inclusion before stress. Overall, the results highlight that a high (14%) inclusion rate of C. vulgaris in feed for Atlantic salmon impairs feed conversion and shifts the intestinal microbiota composition in digesta and mucosa. Weekly feeding of C. vulgaris proves a viable approach in improving protein retention and improving transcriptional resilience towards oxidative stress in increasingly intensive production systems. Thereby this study may motivate future studies on optimizing temporal feeding schedules for health-promoting aquafeeds.

Integrated metabolomics and gut microbiota analysis to explore potential mechanism of Qi-Huo-Yi-Fei formula against chronic obstructive pulmonary disease

Metabolic disorders and gut microbiota dysbiosis contribute to the complicated pathology of chronic obstructive pulmonary disease (COPD). Qi-Huo-Yi-Fei formula (QHYFF) is a Chinese medicine prescription for COPD treatment and has showed beneficial clinical effects, but the underlying mechanism remains elusive. This study integrated metabolomics and gut microbiota analysis to explore potential mechanism of QHYFF against COPD. The therapeutic effects of QHYFF were evaluated using a murine model of COPD induced by cigarette smoke and lipopolysaccharide. QHYFF effectively improved pulmonary function, suppressed inflammation, and relieved lung pathological changes. Serum and urine metabolomics analysis identified 19 differential metabolites, such as L-tyrosine, epinephrine, dopamine, hypotaurine, citric acid, L-tryptophan and indoleacrylic acid, involving tyrosine metabolism, taurine and hypotaurine metabolism, citrate cycle and tryptophan metabolism. QHYFF also enriched Bifidobacterium, Blautia, Faecalibaculum and Parasutterella. Moreover, Spearman's correlation analysis showed that discriminative metabolites and bacteria were closely correlated with efficacy indices. The findings indicated that QHYFF could be an effective therapeutic measure against COPD by regulating metabolism and gut microbiota.

Enhanced phytoremediation of vanadium using coffee grounds and fast-growing plants: Integrating machine learning for predictive modeling

Vanadium (V) contamination posed a significant environmental challenge, while phytoremediation offered a sustainable solution. Phytoremediation performance was often limited by the slow growth cycles of traditional plants. A novel approach to enhancing V phytoremediation by integrating coffee grounds with fast-growing plants such as barley grass, wheat grass, and ryegrass was investigated in this study. The innovative use of coffee grounds leveraged not only their nutrient-rich composition but also their ability to reduce oxidative stress in plants, thereby significantly boosting phytoremediation efficiency. Notably, ryegrass achieved 48.7% V5+ removal within 6 d with initial 20 mg/L V5+ (0.338 mg/L·d·g ryegrass). When combined with coffee grounds, V5+ removal by using wheat grass increased substantially, rising from 30.51% to 62.91%. Gradient Boosting and XGBoost models, trained with optimized parameters including a learning rate of 0.1, max depth of 3, and n_estimators of 300, were employed to predict and optimize V5+ concentrations in the phytoremediation process. These models were evaluated using mean squared error (MSE) and coefficient of determination (R2) metrics, achieving high predictive accuracy (R2 = 0.95, MSE = 1.20). Feature importance analysis further identified the initial V5+ concentration and experimental duration as the most significant factors influencing the model's predictions. The addition of coffee grounds not only mitigated the stress of heavy metals on ryegrass, leading to significant reductions in CAT (87.2%), POD (98.8%), and SOD (39.2%) activities in ryegrass roots, but also significantly altered the microbial community abundance in the plant roots. This research provided an innovative enhancement to traditional phytoremediation methods, and established a new paradigm for using machine learning to predict and optimize V5+ remediation outcomes. The effectiveness of this technology in multi-metal polluted environments warrants further investigation in the future.

Effects of cortisone in zebrafish (Danio rerio): Insights into gut microbiota interactions and molecular mechanisms underlying DNA damage and apoptosis

Cortisone can enter aquatic ecosystems and pose a risk to organisms therein. However, few studies have explored the effects of cortisone on the gut microbiota of aquatic organisms. Here, we exposed zebrafish (Danio rerio) to cortisone at environmentally relevant concentrations (5.0, 50.0, or 500.0 ng L-1) for 60 days to explore its toxicological effects and their association with gut microbiota changes. The terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling assay revealed that exposure to 50 ng L-1 cortisone significantly increased the intestinal cell apoptosis rate, 8-hydroxydeoxyguanosine contents, and caspase-3 and caspase-8 activities. Moreover, the transcriptome analysis results demonstrated a notable downregulation in the expression of most differentially expressed genes associated with apoptosis pathways, as well as changes in DNA replication, oxidative stress, and drug metabolism pathways; these results indicated the occurrence of cortisone-induced stress response in zebrafish. Molecular docking analysis revealed that cortisone can bind to caspase-3 through hydrogen bonds and hydrophobic interactions but that no such interactions occur between cortisone and caspase-8. Thus, cortisone may induce oxidative DNA damage and apoptosis by activating caspase-3. Finally, the 16S rRNA sequencing results demonstrated that cortisone significantly affected microbial community structures and functions in the intestinal ecosystem. These changes may indicate gut microbiota response to cortisone-induced intestinal damage and inflammation. In conclusion, the current results clarify the mechanisms underlying intestinal response to cortisone exposure and provide a basis for evaluating the health risks of cortisone in animals.

Gut microbiome and antibiotic resistance genes in plateau model animal (Ochotona curzoniae) exhibit a relative stability under cold stress

Antibiotic resistance genes (ARGs) carried by gut pathogens may pose a threat to the host and ecological environment. However, few studies focus on the effects of cold stress on intestinal bacteria and ARGs in plateau animals. Here, we used 16S rRNA gene sequencing and gene chip technique to explore the difference of gut microbes and ARGs in plateau pika under 4 °C and 25 °C. The results showed that tetracycline and aminoglycoside resistance genes were the dominant ARGs in pika intestine. Seven kinds of high-risk ARGs (aadA-01, aadA-02, ermB, floR, mphA-01, mphA-02, tetM-02) existed in pika's intestine, and cold had no significant effect on the composition and structure of pika's intestinal ARGs. The dominant phyla in pika intestine were Bacteroidetes and Firmicutes. Cold influenced 0.47 % of pika intestinal bacteria in OTU level, while most other bacteria had no significant change. The diversity and community assembly of intestinal bacteria in pika remained relatively stable under cold conditions, while low temperature decreased gut microbial network complexity. In addition, low temperature led to the enrichment of glycine biosynthesis and metabolism-related pathways. Moreover, the correlation analysis showed that eight opportunistic pathogens (such as Clostridium, Staphylococcus, Streptococcus, etc.) detected in pika intestine might be potential hosts of ARGs.

Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study

Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an intersubject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of oil-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.

rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA

Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well.

IMPORTANCE

We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research.

A novel clinically relevant human fecal microbial transplantation model in humanized mice

The intact immune system of mice exhibits resistance to colonization by exogenous microorganisms, but the gut microbiota profiles of the humanized mice and the patterns of human fecal microbiota colonization remain unexplored. Humanized NCG (huNCG) mice were constructed by injected CD34 +stem cells. 16S rRNA sequencing and fecal microbiota transplantation (FMT) technologies were used to detect the differences in microbiota and selective colonization ability for exogenous community colonization among three mice cohorts (C57BL/6J, NCG, and huNCG). Flow cytometry analysis showed that all huNCG mice had over 25% hCD45 +in peripheral blood. 16S rRNA gene sequence analysis showed that compared with NCG mice, the gut microbiota of huNCG mice were significantly altered. After FMT, the principal coordinates analysis (PCoA) showed that the gut microbial composition of huNCG mice (huNCG-D9) was similar to that of donors. The relative abundance of Firmicutes and Bacteroidetes were significantly increased in huNCG mice compared to NCG mice. Further comparison of ASV sequences revealed that Bacteroides plebeius, Bacteroides finegoldii, Escherichia fergusonii, Escherichia albertii, Klebsiella pneumoniae, and Klebsiella variicola exhibited higher abundance and stability in huNCG mice after FMT. Furthermore, PICRUSt2 analysis showed that huNCG mice had significantly enhanced metabolism and immunity. This study demonstrated that humanized mice are more conducive to colonization within the human gut microbiota, which provides a good method for studying the association between human diseases and microbiota.IMPORTANCEThe gut microbiota and biomarkers of humanized mice are systematically revealed for the first time. The finding that human fecal microbiota colonize humanized mice more stably provides new insights into the study of interactions between immune responses and gut microbiota.

Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.

Guideline for designing microbiome studies in neoplastic diseases

Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.

Characterizing the gastrointestinal microbiome diversity in endangered Malayan Siamang (Symphalangus syndactylus): Insights into group composition, age variability and sex-related patterns

BACKGROUND

The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus.

METHODS

This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region.

RESULTS

A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut.

CONCLUSIONS

This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.

Microbial-mediated metal(loid) immobilization in mulch-covered tailings

Mulch coverage of mining tailings can create anaerobic conditions and consequently establish an anoxic environment that promotes the metabolic processes of anaerobic microorganisms. This anoxic environment has the potential to decrease heavy metal mobility and bioavailability. While tailings exposed to sunlight have been extensively studied, research on the effects of microbial-mediated geochemical cycling of heavy metals in mulch-covered tailings is scarce. This study aimed to examine the effects of mulch coverage-induced alterations in the structures of tailing microbial communities on the biogeochemical processes associated with heavy metals. Mulch coverage significantly reduced the pH of the tailings and the tailings exhibited heavy metal bioavailability. Random forest analysis demonstrated that mulch coverage-induced changes in the As/Cd-contaminated fractions and nutrients (total organic carbon and total nitrogen) were the most crucial predictors of microbial diversity and ecological clusters in the tailings. Notably, different from direct metal(loid) immobilization, mulch coverage can facilitate heavy metal immobilization in tailings by promoting microbial-mediated Fe, S, and As reduction. Overall, this study demonstrated that mulch coverage of tailings contributed to a reduction in heavy metal mobilization, which can be attributed to shifts in microbial-mediated Fe, S, and As reduction processes.The study provides valuable insights into the potential of mulch coverage as a remediation strategy and underscores the importance of microbial-mediated processes in managing heavy metal pollution in tailing systems.

The influence of bioturbator activity on sediment bacterial structure and function is moderated by environment

Bioturbation in coastal sediments plays a crucial role in biogeochemical cycling. However, a key knowledge gap is the extent to which bioturbation influences bacterial community diversity and ecosystem processes, such as nitrogen cycling. This study paired bacterial diversity, bioturbation activity and in situ flux measurements of oxygen and nitrogen from bioturbated sediments at six estuaries along the East coast of Australia. Bacterial community diversity, composition and predicted functional profiles were similar across burrow and surface sediments but were significantly influenced by bioturbator activity (measured as number of burrows) at sites with higher fine grain content. Sediment oxygen demand increased with bioturbator activity but changes in nitrogen cycling (as measured by fluxes and predicted bacterial functional gene analysis) were more spatially variable and were unrelated to bioturbator activity and bacterial community shifts. This study highlights how bioturbator activity influences bacterial community structure and functioning and what implications this has for biogeochemical cycles in estuarine sediments.

Dysbiosis of the gut microbiota in glioblastoma patients and potential biomarkers for risk assessment

BACKGROUND

The significant death rate of glioblastoma is well-known around the world. The link between gut microbiota and glioma is becoming more studied. The goal of this study was to look at the relationships between intestinal flora and glioblastoma, and to provide a new perspective for the diagnosis as well as treatment of glioblastoma.

METHODS

Fecal samples from 80 participants with glioblastoma (n = 40) and healthy individuals (n = 40) in this study were collected as well as analyzed utilizing 16S rRNA gene amplicon sequencing in order to characterize the gut microbial community.

RESULTS

Each group has its own microbial community, and the microbial environment of glioblastoma patients had lower richness and evenness. The structure of gut microbiota community in glioblastoma patients showed profound changes, which includes the increase of pathogens in Fusobacteria and Bacteroidetes, and the reduction of probiotic bacteria in Firmicutes, Actinobacteria and Verrucomicrobia. Meanwhile, the significant correlations and clustering of OTUS (operational taxonomic units) in glioblastoma patients were discovered, and a biomarker panel (Fusobacterium, Escherichia/Shigella, Ruminococcus gnavus group, Lachnospira, Akkermansia, Parasutterella) had been used to discriminate the patients with glioblastoma from the healthy subjects (AUC: 0.80). Furthermore, the glioblastoma group exhibited multiple disturbed pathways through KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, particularly in genetic information processing. Moreover, the prediction of phenotypic characteristics of microbiome proposed that the glioblastoma patients might have more Gram-negative bacteria and opportunistic pathogens than the healthy controls.

CONCLUSIONS

When compared to healthy people, glioblastoma sufferers have a different host-microbe interaction. Furthermore, certain types of intestinal flora could be regarded as biomarkers and drug targets for the diagnosis as well as treatment of glioblastomas.

Airway bacterial microbiome signatures correlate with occupational pneumoconiosis progression

Recent evidence has pinpointed a key role of the microbiome in human respiratory health and disease. However, significant knowledge gaps still exist regarding the connection between bacterial communities and adverse effects caused by particulate matters (PMs). Here, we characterized the bacterial microbiome along different airway sites in occupational pneumoconiosis (OP) patients. The sequencing data revealed that OP patients exhibited distinct dysbiosis in the composition and function of the respiratory microbiota. To different extents, there was an overall increase in the colonization of microbiota, such as Streptococcus, implying a possible intrusion pathway provided by exogenous PMs. Compared to those of healthy subjects, unhealthy living habits (i.e., smoking) had a greater impact on microbiome changes in OP patients. Importantly, the associations between the bacterial community and disease indicators indicated that specific bacterial species, including Prevotella, Actinobacillus, and Leptotrichia, might be surrogate markers of OP disease progression. Collectively, our results highlighted the potential participation of the bacterial microbiota in the pathogenesis of respiratory diseases and helped in the discovery of microbiome-based diagnostics for PM-induced disorders.

Microbial succession in different years of pit mud from a distillery in Sichuan for Nong-xiang Baijiu fermentation

Microbial community and succession of 5-, 20-, and 50-year pit mud (PM) were uncovered in this study. The results showed that Bacteroidetes, Firmicutes and Ascomycota were dominant phyla in these PM samples. Interestingly, most sequences could not be classified into fungal taxa at the genus level by UNITE Database, the diversity and richness of bacteria in these PMs were higher than that of fungi. It was noteworthy that both 20-year and 50-year PMs exhibited higher abundances of Caproiciproducens and Petrimonas when compared with 5-year PM. While higher proportions of Lactobacillus and Acinetobacter were observed in the 5-year PM. Furfermore, these PMs microbiota mainly involved biosynthesis, degradation, and generation of precursor metabolites, which contributed to carbon cycling of Nong-xiang Baijiu anaerobic fermentation. Taken together, lactic acid bacteria depletion and caproic acid bacteria accumulation might be an important succession trend of PM microbiota during the long-term fermentation of Chinese Nong-xiang Baijiu.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01558-4.

Impact of wheat processing on growth, serum biochemistry, and ruminal microbiota in sheep (Ovis aries)

This study investigated the impact of wheat processing methods (wheat flour vs wheat pellets) on the growth performance, serum biochemical parameters, and rumen microbiome composition in sheep. Results indicated that feeding of wheat flour resulted in significantly higher terminal weight and average daily gain (P < 0.05) and lower cholesterol and ALP04 levels (P < 0.05) in sheep compared to those fed wheat pellets. Analysis of 16s rDNA high-throughput sequencing data revealed significantly higher microbial richness (Chao1 index) in the rumen of sheep fed wheat flour (P < 0.05), even though the phylum-level composition dominated by Firmicutes, Bacteroidetes, and Proteobacteria was similar in both groups of sheep. Notably, sheep fed wheat flour were found to have a significantly higher relative abundance of Bacteroidetes (P < 0.05). At the genus level, Succinivibrionaceae_UCG-001 and Prevotella_1 were significantly more abundant in the rumen of sheep fed wheat flour (P < 0.05). Correlation analysis identified that both terminal weight and average daily gain were positively correlated with ruminal abundance of Bacteroidetes and Prevotella_1, while ALP04 was negatively correlated with the abundance of these taxa. Functional prediction using PICRUSt2 indicated enrichment of pathways related to the ABC-type glycerol-3-phosphate transport system, and periplasmic components in both wheat flour and pellet fed sheep. Overall, these findings suggest that dietary wheat flour modulates rumen microbiota composition, and improves growth performance in sheep.

Inhalation of 2,2',5,5'-tetrachlorobiphenyl (PCB52) causes changes to the gut microbiome throughout the gastrointestinal tract

Polychlorinated biphenyls (PCBs), such as PCB52, are hazardous environmental contaminants present in indoor and outdoor environments. Oral PCB exposure affects the colon microbiome; however, it is unknown if inhalation of PCBs alters the intestinal microbiome. We hypothesize that sub-acute inhalation of PCB52 affects microbial communities depending on the location in the (GI) gastrointestinal tract and the local profiles of PCB52 and its metabolites present in the GI tract following mucociliary clearance and biliary or intestinal excretion. Sprague-Dawley rats were exposed via nose-only inhalation 4 h per day, 7 days per week, for 4 weeks to either filtered air or PCB52. After 28 days, differences in the microbiome and levels of PCB52 and its metabolites were characterized throughout the GI tract. PCB52 inhalation altered taxa abundances and predicted functions altered throughout the gut, with most alterations occurring in the large intestine. PCB52 and metabolite levels varied across the GI tract, resulting in differing PCB × microbiome networks. Thus, the presence of different levels of PCB52 and its metabolites in different parts of the GI tract has varying effects on the composition and predicted function of microbial communities. Future studies need to investigate whether these changes lead to adverse outcomes.

Regulation of gut microbiota and serum neurotransmitters in mice by Streptococcus thermophilus GA8- and Lacticaseibacillus rhamnosus HAO9-fermented milk containing high levels of gamma-aminobutyric acid

BACKGROUND

Gamma-aminobutyric acid (GABA) is an important neurotransmitter in the human body, with several negative emotions reported as being associated with GABA dysregulation. This study investigates the safety and modulatory effects of GABA-enriched milk, fermented by Streptococcus thermophilus GA8 and Lacticasebacillus rhamnosus HAO9, on the gut microbiota and neurotransmitter profiles in mice.

RESULTS

Through rigorous culturing and fermentation processes, we achieved consistent GABA production in milk, with concentrations reaching 4.6 and 8.5 g L-1 for GA8-fermented and co-fermented milk, respectively, after 48 h. Using SPF male C57BL/6J mice, we administered either mono-culture or combined-culture milk treatments and monitored physiological impacts. The treatments did not affect mouse body weight but induced significant changes in gut microbiota composition. Beta diversity analysis revealed distinct microbial profiles between treatment groups, highlighting fermentation-specific microbial shifts, such as an increase in Verrucomicrobia for the GA8 group and a modulation in Saccharibacteria_genera_incertae_sedis for the GA8 + HAO9 group. Serum neurotransmitter levels were elevated in both treatment groups, with significant increases in l-glutamine, l-tryptophan and, notably, serotonin hydrochloride in the GA8 + HAO9 group. Correlation analysis identified a positive association between specific bacterial genera and neurotransmitter levels, suggesting a probiotic effect on neuroactive substances.

CONCLUSION

These findings suggest that fermented milk has potential as a probiotic supplement for mood improvement and stress relief, highlighting its role in modulating the gut-brain axis. © 2024 Society of Chemical Industry.

Neonatal gut microbiota profile and the association with retinopathy of prematurity in preterm infants

BACKGROUND

To explore the role of gut microbiota in preterm infants at high risk of developing retinopathy of prematurity (ROP).

METHODS

Preterm infants with gestational age (GA) < 32 weeks and/or birth weight (BW) < 1500 g born between 2020 and 2021 were prospectively enrolled. Their faecal samples were collected and analysed at different postnatal ages of life using 16S rRNA gene sequencing on the Miseq platform. The main outcome measures were the microbial diversity, taxonomy, relative abundance, bacterial predicted functional analysis, and their associations with different ROP groups. Subgroup analyses were performed by matching their GA and BW across different ROP groups.

RESULTS

A total of 268 stool samples were collected from 110 preterm infants, including 13 with type 1 ROP, 44 with type 2 or mild ROP, and 53 without ROP. Type 1 ROP showed no significant difference in microbial diversity up to 8 postnatal weeks (p = 0.057), while type 2 and no ROP groups displayed increased diversity (p = 0.0015 and p = 0.049, respectively). Bifidobacterium genera was notably less abundant in type 1 ROP group at first postnatal week (p = 0.022) and remained low in subsequent weeks. Predicted functional analysis revealed enriched pathways in membrane transport, carbohydrate metabolism, amino acid metabolism, and replication and repair.

CONCLUSIONS

Reduced gut microbial diversity may be associated with ROP development in high-risk preterm infants. Further research is needed to comprehend how early-life Bifidobacterium reduction affects metabolism and how targeting microbiome may help for ROP prevention and management.

Standardization of gut microbiome analysis in sports

The gut microbiome plays a significant role in physiological functions such as nutrient processing, vitamin production, inflammatory response, and immune modulation, which, in turn, are important contributors to athlete health and performance. To date, the interpretation, discussion, and visualization of microbiome results of athletes are challenging, due to a lack of standard parameters and reference data for collection and comparison. The purpose of this perspective piece is to provide researchers with an easy-to-understand framework for the collection, analysis, and data management related to the gut microbiome with a specific focus on athletic populations. In the absence of a consensus on microbiome research in the sports field, we hope that these considerations serve as foundational "best practice." Adherence to these standard operating procedures will accelerate the path toward improving the quality of data and ultimately our understanding of the influence of the gut microbiome in sport settings.

Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction

Background

Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.

Methods

High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.

Results

We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.

Conclusion

Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.

Microbial Community Structure and Metabolic Function in the Venom Glands of the Predatory Stink Bug, Picromerus lewisi (Hemiptera: Pentatomidae)

The predatory stink bug, Picromerus lewisi (Hemiptera: Pentatomidae), is an important and valuable natural enemy of insect pests in their ecosystems. While insects are known to harbor symbiotic microorganisms, and these microbial symbionts play a crucial role in various aspects of the host's biology, there is a paucity of knowledge regarding the microbiota present in the venom glands of P. lewisi. This study investigated the venom glands of adult bugs using both traditional in vitro isolation and cultural methods, as well as Illumina high-throughput sequencing technology. Additionally, the carbon metabolism of the venom gland's microorganisms was analyzed using Biolog ECO metabolic phenotyping technology. The results showed 10 different culturable bacteria where the dominant ones were Enterococcus spp. and Lactococcus lactis. With high-throughput sequencing, the main bacterial phyla in the microbial community of the venom glands of P. lewisi were Proteobacteria (78.1%) and Firmicutes (20.3%), with the dominant bacterial genera being Wolbachia, Enterococcus, Serratia, and Lactococcus. At the fungal community level, Ascomycota accounted for the largest proportion (64.1%), followed by Basidiomycota (27.6%), with Vishniacozyma, Cladosporium, Papiliotrema, Penicillium, Fusarium, and Aspergillus as the most highly represented fungal genera. The bacterial and fungal community structure of the venom glands of P. lewisi exhibited high species richness and diversity, along with a strong metabolism of 22 carbon sources. Functional prediction indicated that the primary dominant function of P. lewisi venom-gland bacteria was metabolism. The dominant eco-functional groups of the fungal community included undefined saprotroph, fungal parasite-undefined saprotroph, unassigned, endophyte-plant pathogen, plant pathogen-soil saprotroph-wood saprotroph, animal pathogen-endophyte-plant pathogen-wood saprotroph, plant pathogen, and animal pathogen-endophyte-epiphyte-plant pathogen-undefined saprotroph. These results provide a comprehensive characterization of the venom-gland microbiota of P. lewisi and demonstrate the stability (over one week) of the microbial community within the venom glands. This study represents the first report on the characterization of microbial composition from the venom glands of captive-reared P. lewisi individuals. The insights gained from this study are invaluable for future investigations into P. lewisi's development and the possible interactions between P. lewisi's microbiota and some Lepidopteran pests.

Bacterial and fungal aerosols in poultry houses: PM2.5 metagenomics via single-molecule real-time sequencing

Microbial aerosol contamination is a common problem in poultry farms, posing potential health risks to poultry and their caretakers. Exploring the distribution and diversity of the microbial community in poultry farm aerosols is crucial for effective mitigation strategies. The composition of bacterial and fungal aerosols is poorly understood, particularly the prevalence of potential pathogenic microorganisms in fine particulate matter (PM2.5) in various types of poultry houses. In this study, 27 PM2.5 samples were collected from 5 chicken houses and 4 duck houses in Shandong Province, China. Species-level diversity of bacterial and fungal components in PM2.5 samples was determined using advanced single-molecule real-time sequencing (SMRT) technology, based on the 16S and internal transcribed spacer 1 (ITS) ribosomal genes. Microbial diversity and community composition varied significantly across the different poultry house. Notably, duck houses had higher concentrations (p < 0.01) of PM2.5 (92.8-143.1 μg/m3) than chicken houses (42.0-56.4 μg/m3). Furthermore, microbial variation in PM2.5 samples was associated with the type of poultry facility. The predominant pathogenic microorganisms included Aspergillus sydowii, Penicillium sp., Aspergillus insolitus, Cladosporium sp., Aspergillus sp., Aspergillus pseudoglaucus, Cladosporium sp. C4092-2-PD1, and Colletotrichum sp., all of which were classified as second category of pathogens. Aspergillus sydowii and Penicillium sp. were the dominant species in chicken houses, while Cladosporium sp., Aspergillus sp., and Aspergillus pseudoglaucus were the dominant species identified in duck houses. To our knowledge, this study is the first to investigate bacterial and fungal diversity in PM2.5 samples collected from various types of poultry houses. These findings advance our understanding of poultry environmental microbiology and have important implications for safeguarding the health of both poultry and their caretakers.

Role of tenofovir dipivoxil in gut microbiota recovery from HBV-infection induced dysbiosis

BACKGROUND

Studies have found dysbiosis of the gut microbiota in individuals infected with the hepatitis B virus (HBV). Tenofovir dipivoxil (TDF) is one of the preferred oral antiviral drugs used for the treatment of chronic hepatitis B (CHB), but the extent to which TDF is able to affect the gut microbiota and inflammatory factors of a patient remains largely unexplored. In this study, we collected stool samples from HBV patients prior to medication and from CHB patients treated with TDF.

RESULTS

The gut microbiota and inflammatory factors were assessed in 42 healthy subjects (HC group), 109 HBV-infected subjects, including 48 CHB patients who were not medicated with nucleoside analogue drugs (No-NAs group), and 61 CHB patients who were medicated with TDF (TDF group). 16 S rRNA sequencing revealed that TDF treatment caused significant changes in the gut microbiota of HBV-infected individuals; however, the gut microbiota of HBV-infected individuals did not fully recover to a pre-dysbiosis state. The relative abundance of Bacteroidota gradually decreased from the HC group to the No-NAs and TDF groups. The relative abundance of Fusobacteriota was significantly higher in the No-NAs group than in the HC group. At the genus level, Dialister, Eubacterium_hallii_group, Halomonas, Collinsella, Sphingomonas, Xanthomonadaceae_unclassified, and Rhizobiaceae_unclassified were overrepresented; while the abundance of Bacteroides and Fusobacterium decreased significantly in the No-NAs and TDF groups.

CONCLUSIONS

This study showed that TDF treatment significantly improved the regulation of the gut microbiota and aided in dysbiosis recovery. We did not observe significant improvement in serum inflammatory factor concentrations, which may be related to the relatively short duration of TDF administration in this study.

Diversified crop rotations improve soil microbial communities and functions in a six-year field experiment

Diversified crop rotations can help mitigate the negative impacts of increased agricultural intensity on the sustainability of agroecosystems. However, the impact of crop rotation diversity on the complexity of soil microbial association networks and ecological functions is still not well understood. In this study, a 6-year field experiment was conducted to evaluate how six different crop rotations change the composition and network complexity of soil microbial communities, as well as their related ecological functions. Microbial traits were measured in six crop rotations with different crop diversity index (CDI) during 2016-2022, including winter wheat-summer maize (CDI 1, WM) as the control, sweet potato→winter wheat-summer maize (CDI 1.5, SpWM), peanut→winter wheat-summer maize (CDI 1.5, PWM), soybean→winter wheat-summer maize (CDI 1.5, SWM), spring maize→winter wheat-summer maize (CDI 1.5, SmWM), and ryegrass-sweet sorghum→winter wheat-summer maize (CDI 2, RSWM). The study findings indicated that diversified crop rotations significantly increased ASV richness of both bacterial and fungal communities after 6-year treatments, and the β-diversity profiles of bacterial and fungal communities significantly distinguished at the year of 2022 from 2016. The relative abundance of Acidobacteria and Chloroflexi was significantly enriched in SpWM rotation at 2022, while Basidiomycota significantly declined in five diversified rotations compared to WM. Diversified crop rotations at 2022 increased the complexity and density of bacterial and fungal networks than 2016. SpWM and PWM rotations had the highest functional groups involved in chemoheterotrophy and saprotroph, respectively. Structural equation modelling (SEM) also revealed that diversified crop rotations increased soil nutrients through improving the composition of bacterial communities and the augmented intricacy of the interconnections within both bacterial and fungal communities. This research underscores the importance of preserving the diversity and ecological functions of soil microorganisms in the nutrient-recycling processes for efficient agricultural practices.

Effects of Interactions between Feeding Patterns and the Gut Microbiota on Pig Reproductive Performance

The feeding mode is an important factor affecting the reproductive performance of pigs. The composition and expression of the intestinal microbiota are closely related to the physiological and biochemical indicators of animals. Therefore, to explore the impact of different feeding patterns on the reproductive performance of pigs, this study collected reproductive performance data from 1607 Yorkshire pigs raised under different feeding patterns and conducted a fixed-effect variance analysis. Among them, 731 were in the artificial feeding (AM) group and 876 were in the feeding station feeding (SM) group. Additionally, 40 Yorkshire sows in the late gestation period were randomly selected from each feeding mode for intestinal microbiota analysis. The results of the analysis showed that, in the AM group, both the number of birth deformities (NBD) and the number of stillbirths (NSB) were significantly greater than they were in the SM group (p < 0.05). Additionally, the total number born (TNB) in the AM group was significantly lower than that in the SM group (p < 0.05). The results of the intestinal microbiota analysis revealed that at the phylum level, there were significant differences in nine bacterial taxa between the AM and SM groups (p < 0.05). At the genus level, the abundance of a variety of beneficial bacteria related to reproductive performance in the SM group was significantly greater than that in the AM group. Finally, fecal metabolomic analysis revealed that the contents of butyric acid, isovaleric acid, valeric acid, and isobutyric acid, which are associated with reproductive performance, in the feces of sows in the SM group were significantly higher than those in the AM group (p < 0.05). These results indicate that different feeding methods can affect the gut microbiota composition of Yorkshire pigs and further influence the reproductive performance of pigs through the gut microbiota-metabolic product pathway. The results of this study provide valuable insights for further exploring the relationships between feeding modes, intestinal microbial composition, and host phenotypes.

Methods for studying microbial acid stress responses: from molecules to populations

The study of how micro-organisms detect and respond to different stresses has a long history of producing fundamental biological insights while being simultaneously of significance in many applied microbiological fields including infection, food and drink manufacture, and industrial and environmental biotechnology. This is well-illustrated by the large body of work on acid stress. Numerous different methods have been used to understand the impacts of low pH on growth and survival of micro-organisms, ranging from studies of single cells to large and heterogeneous populations, from the molecular or biophysical to the computational, and from well-understood model organisms to poorly defined and complex microbial consortia. Much is to be gained from an increased general awareness of these methods, and so the present review looks at examples of the different methods that have been used to study acid resistance, acid tolerance, and acid stress responses, and the insights they can lead to, as well as some of the problems involved in using them. We hope this will be of interest both within and well beyond the acid stress research community.

The impact of carvacrol on the larval gut bacterial structure and function of Lymantria dispar

Introduction

The gut bacteria of insects play an important role in regulating their metabolism, immune system and metabolizing pesticides. Our previous results indicate that carvacrol has certain gastric toxic activity on Lymantria dispar larvae and affects their detoxification metabolism at the mRNA level. However, the impact of carvacrol on the gut bacteria of L. dispar larvae has been unclear.

Methods

In this study, the 16S rRNA sequencing technology was used to sequence and analyze the gut bacteria of the larvae which were exposed with sublethal concentration (0.297 mg/mL) and median lethal concentration (1.120 mg/mL), respectively.

Results

A total of 10 phyla, 16 classes, 47 orders, 72 families, 103 genera, and 135 species were obtained by using a 97% similarity cutoff level. The dominant bacterial phyla in the gut of the L. dispar larvae are Firmicutes and Proteobacteria. The treatment with carvacrol can significantly affect the structure of gut bacteria in the larvae of the L. dispar. At both doses, carvacrol can shift the dominant gut bacteria of the larvae from Proteobacteria to Firmicutes. At the genus level, two doses of carvacrol can significantly enhance the relative abundance of probiotic Lactobacillus in the gut of L. dispar larvae (p ≤ 0.01). Additionally, significant differences were observed among the five bacterial genera Burkholderia-Caballeronia-Paraburkholderia, Anoxybacillus, Pelomonas, Mesorhizobium (p ≤ 0.05). The analysis of α-diversity and β-diversity indicates that the treatment with carvacrol at two doses significantly affect the bacterial richness and diversity in the larvae. However, the results of functional classification prediction (PICRUSt) indicate that carvacrol significantly down-regulate 7 functions, including Energy metabolism, Cell growth and death, and up-regulate 2 functions, including Carbohydrate metabolism and Membrane transport. The network analysis indicates that the correlation between gut bacteria also has been changed. In addition, the insecticidal activity results of carvacrol against L. dispar larvae with gut bacteria elimination showed that gut bacteria can reduce the insecticidal activity of carvacrol against L. dispar larvae.

Discussion

This study provides a theoretical foundation for understanding the role of gut bacteria in detoxifying plant toxins and conferring pesticide resistance.

Intestinal-level anti-inflammatory bioactivities of whole wheat: Rationale, design, and methods of a randomized, controlled, crossover dietary trial in adults with prediabetes

Randomized controlled trials (RCT) demonstrate that whole wheat consumption improves glycemia. However, substantial inter-individual variation is often observed, highlighting that dietary whole grain recommendations may not support the health of all persons. The objective of this report is to describe the rationale and design of a planned RCT aimed at establishing the gut microbiota and metabolome signatures that predict whole wheat-mediated improvements in glucose tolerance in adults with prediabetes. It is hypothesized that a controlled diet containing wheat bread (WHEAT; 160 g/day) compared with refined bread (WHITE) will improve glucose tolerance in a gut microbiota-mediated manner. Biospecimens will be collected before and after each 2-week study arm. Testing for oral glucose tolerance and gastrointestinal permeability will be performed post-intervention. Assessments will include oral glucose tolerance (primary outcome) and secondary outcomes including gut microbiota, targeted and untargeted metabolomics of fecal and plasma samples, intestinal and host inflammatory responses, and intestinal permeability. WHEAT is predicted to alleviate glucose intolerance by shifting microbiota composition to increase short-chain fatty acid-producing bacteria while reducing populations implicated in intestinal inflammation, barrier dysfunction, and systemic endotoxemia. Further, benefits from WHEAT are anticipated to correlate with gut-level and systemic metabolomic responses that can help to explain the expected inter-individual variability in glucose tolerance. Thus, knowledge gained from integrating multi-omic responses associating with glucose tolerance could help to establish a precision nutrition-based framework that can alleviate cardiometabolic risk. This framework could inform novel dietary whole grain recommendations by enhancing our understanding of inter-individual responsiveness to whole grain consumption.

Metrological evaluation of DNA extraction method effects on the bacterial microbiome and resistome in sputum

Targeted high-throughput sequencing (HTS) has revolutionized the way we look at bacterial communities. It can be used for the species-specific detection of bacteria as well as for the determination of the microbiome and resistome and can be applied to samples from almost any environment. However, the results of targeted HTS can be influenced by many factors, which poses a major challenge for its use in clinical diagnostics. In this study, we investigated the impact of the DNA extraction method on the determination of the bacterial microbiome and resistome by targeted HTS using principles from metrology and diagnostics such as repeatability and analytical sensitivity. Sputum samples spiked with Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa at three different concentrations (103-106 cells/mL) were used. DNA was extracted from each sample on 2 separate days in three replicates each using three different extraction methods based on cetrimonium bromide, magnetic beads, and silica membranes. All three spiked bacteria were detected in sputum, and the DNA extraction method had no significant effect on detection. However, the DNA extraction method had significant effects on the composition of the microbiome and the resistome. The sequencing results were repeatable in the majority of cases. The silica membrane-based DNA extraction kit provided the most repeatable results and the highest diversity of the microbiome and resistome. Targeted HTS has been shown to be a reliable tool for determining the microbiome and resistome; however, the method of DNA extraction should be carefully selected to minimize its impact on the results.

IMPORTANCE

High-throughput sequencing (HTS) is one of the crucial new technologies that gives us insights into previously hidden parts of microbial communities. The DNA extraction method is an important step that can have a major impact on the results, and understanding this impact is of paramount importance for their reliable interpretation. Our results are of great value for the interpretation of sputum microbiome and resistome results obtained by targeted HTS. Our findings allow for a more rational design of future microbiome studies, which would lead to higher repeatability of results and easier comparison between different laboratories. This could also facilitate the introduction of targeted HTS in clinical microbiology for reliable identification of pathogenic bacteria and testing for antimicrobial resistance (AMR). As AMR is a major threat to public health, the improved methods for determining AMR would bring great benefits to both the healthcare system and society as a whole.

Intratumoral and fecal microbiota reveals microbial markers associated with gastric carcinogenesis

Background

The relationship between dysbiosis of the gastrointestinal microbiota and gastric cancer (GC) has been extensively studied. However, microbiota alterations in GC patients vary widely across studies, and reproducible diagnostic biomarkers for early GC are still lacking in multiple populations. Thus, this study aimed to characterize the gastrointestinal microbial communities involved in gastric carcinogenesis through a meta-analysis of multiple published and open datasets.

Methods

We analyzed 16S rRNA sequencing data from 1,642 gastric biopsy samples and 394 stool samples across 11 independent studies. VSEARCH, QIIME and R packages such as vegan, phyloseq, cooccur, and random forest were used for data processing and analysis. PICRUSt software was employed to predict functions.

Results

The α-diversity results indicated significant differences in the intratumoral microbiota of cancer patients compared to non-cancer patients, while no significant differences were observed in the fecal microbiota. Network analysis showed that the positive correlation with GC-enriched bacteria increased, and the positive correlation with GC-depleted bacteria decreased compared to healthy individuals. Functional analyses indicated that pathways related to carbohydrate metabolism were significantly enriched in GC, while biosynthesis of unsaturated fatty acids was diminished. Additionally, we investigated non-Helicobacter pylori (HP) commensals, which are crucial in both HP-negative and HP-positive GC. Random forest models, constructed using specific taxa associated with GC identified from the LEfSe analysis, revealed that the combination of Lactobacillus and Streptococcus included alone could effectively discriminate between GC patients and healthy individuals in fecal samples (area under the curve (AUC) = 0.7949). This finding was also validated in an independent cohort (AUC = 0.7712).

Conclusions

This study examined the intratumoral and fecal microbiota of GC patients from a dual microecological perspective and identified Lactobacillus, Streptococcus, Roseburia, Faecalibacterium and Phascolarctobacterium as intratumoral and intestinal-specific co-differential bacteria. Furthermore, it confirmed the validity of the combination of Lactobacillus and Streptococcus as GC-specific microbial markers across multiple populations, which may aid in the early non-invasive diagnosis of GC.

Palmatine protects against atherosclerosis by gut microbiota and phenylalanine metabolism

Accumulating evidence illuminated that gut microbiota directly modulates the development of atherosclerosis (AS) through interactions with metaflammation. The natural bioactive isoquinoline alkaloid palmatine (PAL), which is extracted from one of the herbs (Coptis chinensis) of the anti-AS formular, is of particular interest due to its pharmacological properties. ApoE-/- mice were administered PAL or vehicle; plaque areas, and stability were assessed by histopathological and immunohistochemistry analysis, serum glycolysis and lipid levels, and inflammation levels were also evaluated. 16S rRNA sequencing and metabolomics analysis were employed to evaluate microbial composition and serum metabolites. Microbial culture experiments were designed to reveal the target microbiota and associated metabolites. Cell culture and transcriptome were performed to elucidate the function of microbial metabolites on THP-1. PAL reduced the area of plaque and necrotic core, improving inflammatory infiltration within plaques, improving glycolipid metabolism, and reducing the levels of serum inflammatory cytokines in a dose-dependent manner. PAL treatment reshaped the composition of the gut microbiota, especially, reducing the relative abundance of Desulfovibrio piger (D. piger) in a dose-dependent manner and serum level of hippuric acid (HA). D. piger was able to convert phenylalanine into 3-phenylpropionic acid (precursor of HA). Finally, we verified HA accelerated the progression of AS and increased the secretions of inflammatory cytokines in vivo and in vitro. In conclusion, PAL exhibited anti-AS effects by regulating the gut microbiota-phenylalanine metabolism axis.

Environmental microbes alleviate antibiotic disturbance on plant endophytes in aquatic microcosms: Prospects for conferring fitness benefits

Antibiotic pollution in water environment is an emerging threat to plant health. Developing efficient strategies to reassemble the antibiotic-tolerating endophytes will confer fitness benefits on host plants to alleviate antibiotic stress. Here, introducing environmental microbes was proved as a promising approach to reshape the antibiotic-tolerating plant endophytes under antibiotic stress in aquatic microcosms. The introduction of environmental microbes effectively relieved antibiotic-driven perturbation on plant endophytes, with reduced changes in bacterial diversity and differential bacterial taxa and functional genes. Moreover, introducing environmental microbes facilitated the enrichment of endophytic bacterial genera and functional genes related to drug metabolism, which possessed the potentials to degrade antibiotics. In addition, environmental microbes boosted antibiotic-reshaped endophytes to form more stable bacterial networks for stronger antibiotic tolerance. In consequence, the decreased growth inhibition of antibiotics on host plants and enhanced antibiotic removal from microcosms were achieved by introducing environmental microbes. These findings pursue environmental microbes as practical resources to assist plants in reshaping the stress-alleviating endophytes, potentially improving plant tolerance to water pollution.

Plant endophyte immobilization technology: A promising approach for chromium-contaminated water and soil remediation

Microbial immobilization technology is considered an efficient bioremediation method for chromium (Cr) pollution. However, it is currently unclear which strain is more beneficial for the remediation of Cr-contaminated water and soil. Therefore, corn straw biochar was used as a carrier to prepare materials for fixing the endophytes Serratia sp. Y-13 (BSR1), Serratia nematodiphila (BSR2), Lysinibacillus sp. strain SePC-36 (BLB1), Lysinibacillus mangiferihumi strain WK63 (BLB2) and the commercial bacteria Shewanella oneidensis MR-1 (BSW). The results demonstrated that, compared with BSW, endophyte-loaded biochar (especially BSR1) was more effective at remediating Cr pollution in water and soil. Endophyte-loaded biochar reduced the abundance of soil pathogenic bacteria, enhanced the number of beneficial plant endophytes, reduced the soil Cr(VI) concentration, improved soil fertility, reduced the plant Cr concentration and improved the yield of lettuce. Redundancy analysis (RDA) and structural equation modelling (PLS-PM) suggested that soil microbes are closely related to soil Cr(VI), plant fresh weight and soil organic matter, whereas endophyte-loaded biochar directly influences plant cell motility pathways by altering plant microbes. This study represents a pioneering investigation into the efficacy of endophyte-loaded biochar as a remediation strategy for Cr pollution.

The fate of sulfamethoxazole in microcosms of the macrophyte Schoenoplectus californicus and its impact on microbial communities

Sulfamethoxazole is a widely used antibiotic frequently found as an environmental pollutant. It can alter microbial communities and increase antibiotic resistance, becoming a public health risk. Constructed wetlands have the potential for removing sulfamethoxazole from polluted waters, but the role of different macrophytes in this process is not well understood. We investigated the fate of sulfamethoxazole and its effect on bacterial communities in microcosms containing Schoenoplectus californicus, an altitude-tolerant macrophyte. Within the first ten hours after introducing sulfamethoxazole (initial concentration 5 mg/L) to the microcosms, the concentration in the liquid phase significantly differed between microcosms with and without S. californicus. However, over the long term (15 and 30 days post-addition), the removal percentage (around 75%) in the liquid phase was not significantly influenced by S. californicus, indicating that sediments might be primarily responsible for removing the antibiotic. The presence of S. californicus promoted algae growth in the microcosms, and we determined that algae contributed to sulfamethoxazole removal from the liquid phase, likely through adsorption. Additionally, we characterized bacterial communities in the microcosm sediments via nanopore sequencing to identify changes following sulfamethoxazole addition. The relative abundance of Proteobacteria increased from 37-46% to 48-99% with the addition of the antibiotic. Conversely, the relative abundance of cyanobacteria decreased significantly after sulfamethoxazole was added (from 17-35% to less than 2%), suggesting it may serve as a biological marker for sulfamethoxazole pollution. In addition, the functional profile of the community was estimated from taxonomic diversity using PICRUST.

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii

Amphibians face the threat of decline and extinction, and their health is crucially affected by the microbiota. Their health and ecological adaptability essentially depend on the diverse microbial communities that are shaped by unique host traits and environmental factors. However, there is still limited research on this topic. In this study, cutaneous (C) and gut (G) microbiota in Rana amurensis (A) and R. dybowskii (D) was analyzed through 16S amplicon sequencing. Groups AC and DC significantly differed in alpha diversity, while the gut groups (AG and DG) showed no such differences. Analyses of Bray-Curtis dissimilarity matrix and unweighted UniFrac distances showed significant differences in cutaneous microbiota between groups AC and DC, but not between groups AG and DG. Stochastic processes significantly influenced the assembly of cutaneous and gut microbiota in amphibians, with a notably higher species dispersal rate in the gut. The predominant phyla in the skin of R. amurensis and R. dybowskii were Bacteroidetes and Proteobacteria, respectively, with significant variations in Bacteroidota. Contrarily, the gut microbiota of both species was dominated by Firmicutes, Proteobacteria, and Bacteroidetes, without significant phylum-level differences. Linear discriminant analysis effect size (LEfSe) analysis identified distinct microbial enrichment in each group. Predictive analysis using phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) revealed the significant functional pathways associated with the microbiota, which indicates their potential roles in immune system function, development, regeneration, and response to infectious diseases. This research underscores the critical impact of both host and environmental factors in shaping amphibian microbial ecosystems and emphasizes the need for further studies to explore these complex interactions for conservation efforts.

A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples

Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.

Metagenomic insights into traditional fermentation of rice-based beverages among ethnic tribes in southern Assam, Northeast India

Introduction

Traditional fermented foods have long been recognized for their numerous health benefits along with their potential to aid in the treatment of gastrointestinal disorders. These fermented foods have been shown to promote gut health and contribute to a longer, healthier life.

Methods

The high-throughput sequencing using the Illumina MiSeq platform was employed to investigate the microbiome communities of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes.

Results

The fermented rice-based beverages were highly predominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria exhibiting the highest relative abundance across all tribes. At genus level, significant abundance of pediococcus, lactobacillus, bacillus, leuconostoc, acetobacter, staphylococcus, delftia, erwinia, klebsiella and chrysebacterium were found amongst these ethnic tribes.

Discussion

Understanding the fermented food microbiome will help to know the relationships between microbial communities and their effect on health of humans amongst the tribes. Furthermore, the use of these fermented products could provide enhanced health benefits to southern Assam region of India.

Deciphering the microbial interactions and metabolic shifts at different COD/sulfate ratios in electro-assisted anaerobic digestion

This research aims to investigate the influence of sulfate on the performance of microbial electrolysis cell-assisted anaerobic digester (MEC-AD) across varying sulfate conditions, including no sulfate and reduced COD/sulfate ratios from 20 to 1. The principal results indicate a gradual decline in methane yield in the MEC-AD from 78.7 ± 2.3 % under no sulfate conditions to 56.2 ± 2.0 % at a COD/sulfate ratio of 1, contrasting with a more substantial decrease in the control reactor (69.9 ± 3.6 % to 32.8 ± 1.5 %). The MEC-AD reactor exhibits heightened resilience to sulfide toxicity, showcasing higher specific methanogenic activities. Key findings suggest that the MEC-AD reactor maintains lower free sulfide concentrations, attributed to its higher pH and potential anodic sulfide oxidation. Additionally, the study reveals the promotion of syntrophic partnerships in the MEC-AD reactor, particularly between sulfate-reducing bacteria (SRB) such as Desulfovibrio, Desulfomicrobium, and Desulfobulbus, and other microbial groups, including hydrogenotrophic methanogens and electroactive bacteria. The integration of these mechanisms highlights the MEC-AD reactor's ability to effectively mitigate sulfate-induced challenges and enhance overall anaerobic digestion performance. This study presents a significant step forward in the development of resilient anaerobic digestion systems capable of efficiently handling sulfate stress.