Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

Gut microbiota development in very preterm infants following fortification of human milk

Very preterm infants (VPIs) are born with an immature gut and predisposed to gut microbiota dysbiosis-related diseases, for example, necrotizing enterocolitis. Although fortification of human milk is required for these infants, the optimal fortifier remains uncertain. Bovine colostrum (BC), rich in protein and bioactive components, could serve as an alternative to conventional fortifiers (CF). The gut microbiota (GM) of 225 VPIs fed human milk fortified with either BC or CF (FortiColos study, NCT03537365) was profiled by 16S rRNA gene amplicon sequencing of fecal samples collected before, and after 1 and 2 weeks of fortification. Birth mode exhibited transient effects on the microbial community structure shortly after birth, with cesarean section-born VPIs dominated by Firmicutes, whereas vaginally born VPIs were dominated by Proteobacteria. This birth mode-derived difference diminished with age and disappeared around 1 month after birth. Fortifier type affected the microbial community structure to a modest extent, but no specific taxa significantly differed between the BC and CF groups. Fecal pH, increased by BC, was positively correlated with Staphylococcus and Corynebacterium and negatively with Bifidobacterium abundance. Change in the relative abundance of Staphylococcus was negatively correlated with body weight gain. Collectively, fortification of human milk with BC or CF does influence the GM of VPIs but only to a modest extent during early life. Birth mode appears to have a significant, but temporary influence on the GM during this period.IMPORTANCEEarly life is a key period for gut microbiota (GM) establishment, where enteral feeding plays a significant role. This is also the case for infants born preterm, who, due to their immature gut, are at a high risk of developing GM dysbiosis-related diseases. Human milk is the optimal feed for preterm infants, but it requires fortification to reach adequate levels of especially protein. Only a few studies have investigated the impact of fortifiers on GM development in preterm infants. Here, we demonstrate that two different bovine milk-based fortifiers, bovine colostrum and a conventional fortifier based on mature bovine milk, exhibit limited effects on the microbial community structure of very preterm infants. These findings suggest that although great care in terms of optimally maturing the preterm infant GM should be taken, the choice of fortifier only has limited impact. In clinical practice, the choice of fortifier can thus be fully focussed on optimizing preterm infant nutrition.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03537365.

Impact of stormwater on biofilm density and microbial community composition in water distribution networks

Harvesting of stormwater and injecting it into aquifers for storage and recovery during high water demand periods is a promising technology for augmenting conventional water reserves. However, little has been known on how stormwater impacts the biofouling of water distribution infrastructure. This study evaluated the effect on harvested and limestone aquifer treated stormwater on biofilm formation in a pilot distribution pipe network compared to an identical drinking water pipe rig. Coupons made of cement, copper and polyvinyl chloride (PVC) pipe materials were installed to each pipe rig and exposed to stormwater or drinking water. The total cell counts determined by flow cytometry on the pilot rig coupons were in the order of 105 to 107 cells/cm2 for both source waters and showed some variation over the duration of the study. The culturable cell counts were somewhat higher for stormwater exposed coupons than for coupons in mains water rig. The total number of thermotolerant coliforms was notably higher on coupons exposed to stormwater than on those exposed to mains water. Considerable differences were observed in the bacterial and eukaryotic communities on coupons made of various materials and exposed to mains water and stormwater using pyrosequencing. Moreover, seasonal variations were observed in community composition and diversity. A number of bacterial and eukaryotic families and genera harbouring potential human pathogens were detected in both mains water and stormwater systems, with larger numbers of genera observed in the latter indicating a potentially increased risk of exposure to pathogens with stormwater. The stormwater system also harboured sulfur reducers, and a greater diversity of iron oxidisers. A number of bacterial genera that contribute to nitrogen cycling were observed in both mains water and stormwater systems. A number of bacteria grazing eukaryotes were detected, indicating that the biofilm communities are quite dynamic and the abundance of bacteria is able to support higher level eukaryotes.

Past and present bacterial communities in deglaciating northern latitude catchments reveal varied soil carbon sequestration potential

Glacier retreat in northern latitudes exposes new landscapes that may develop soils and ecosystems, which in turn may sequester carbon and serve as a negative climate change feedback. Proglacial soil development and landscape evolution were investigated using transects from three high-latitude glacial systems (Tarfala, Sweden; Vatnajökull, Iceland; Zackenberg, Greenland). Soil samples were analysed for organic carbon (OC) concentration, bacteriohopanepolyol biomarkers (BHPs, membrane lipids that trace major microbial groups), and 16S rRNA gene sequencing. Soil and sediment samples from Sweden showed lower OC concentrations (0.27 ± 0.26 wt%) than deposits from Iceland (1.59 ± 2.12 wt%) and Greenland (1.62 ± 1.54 wt%). Highest OC concentrations were from moraines exposed for several millennia, while recently deglaciated areas in Sweden and Iceland had the lowest OC values. Higher fractional abundance of soil-specific BHPs down-valley (up to 30 % in Greenland), and matching increases in the R'soil index (up to 0.37 in Greenland), suggest soils are gradually developing in recently deglaciated areas, with a stable soil microbial community observed in some soils from Iceland and Greenland. Microbial communities stabilized quickly, adapting to the new environment. Acidobacteria, Actinobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Verrucomicrobia were the most relatively abundant phyla identified in deglaciated areas, while candidate phylum Dormibacteraeota had high concentrations in samples from Sweden. Linking organic biomarkers with bacterial communities suggests that soil-marker BHPs were produced by Rhodospirillaceae and may have been produced by Bradyrhizobiaceae and Hyphomicrobiaceae. However, despite some similarities in microbial communities, differences in soil development suggest that the evolution of deglaciating landscapes and their impact on the global carbon cycle may vary substantially.

Herbal formula alleviates heat stress by improving physiological and biochemical attributes and modulating the rumen microbiome in dairy cows

Heat stress significantly impacts dairy cow productivity, health, and welfare. This study evaluated a self-developed herbal formula as a dietary intervention to mitigate heat stress. A total of 198 lactating cows were divided into two groups: a Control group receiving standard total mixed rations and a Herbs group supplemented with herbal formula for 60 days. Various parameters were assessed, including milk yield and composition, antioxidant capacity, immune responses, stress-related gene expression, and rumen microbial composition. Compared to the Control group, cows in the Herbs group showed improved feed intake, milk yield and quality, rumination frequency, and enhanced antioxidant activity and immune response. Rumen microbiome analysis revealed a reduced relative abundance of Proteobacteria and Ochrobactrum in the Herbs group, along with an enrichment of beneficial genera such as Lachnospira. Functional predictions indicated that the Herbs group exhibited enhanced glycolysis/gluconeogenesis, pyruvate metabolism, and starch and sucrose metabolism, reflecting improved fermentation efficiency and energy utilization. In conclusion, the herbal formula improved physiological and biochemical attributes, boosted antioxidant and immune responses, and modulated the rumen microbiome, contributing to the alleviation of heat stress in dairy cows. These findings highlight its potential as a natural dietary strategy to support dairy cow health and productivity under heat stress conditions.

Enhancing Growth and Modulation of Gut Microbiota in Red Hybrid Tilapia (Oreochromis sp.) with Host-Associated Leuconostoc lactis as Feed Additive

Economic sustainability and the emergence of infectious diseases remain critical challenges in tilapia aquaculture. Lactic acid bacteria (LAB) are well-known feed additives with probiotic effects in improving overall performance of livestock. This study evaluated the effects of host-associated probiotic, Leuconostoc lactis TARicum AI2, on growth performance, antioxidant, immune responses, and gut microbiota of red hybrid tilapia (Oreochromis sp.) by conducting an 86-day feeding trial. The probiotic, previously characterised for its beneficial traits, was coated on commercial feed at a concentration of 109 CFU g-1. Results showed tilapia fed with probiotic had significant improvement in feed conversion ratio (FCR) and protein efficiency ratio (PER) compared to the control group. Upregulation of cytokine expressions was observed in the probiotic group. Gut microbiota analysis revealed an increased abundance of the genera Clostridium and Leuconostoc in the probiotic-fed tilapia. Beta-diversity indices proved exclusive groups of bacteria present in specific diet only. In conclusion, L. lactis strain TARicum AI2 is a potential probiotic candidate in promoting growth in tilapia as the results suggested it could improve FCR and PER. Feed with lower FCR and higher PER could help tilapia farmers in reducing feed cost, which accounted for the major portion of their production cost. This further enables them to achieve cost-effective, enhanced productivity and economic sustainability in a long run.

Cross-validation for training and testing co-occurrence network inference algorithms

BACKGROUND

Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.

RESULTS

Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.

CONCLUSIONS

Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.

Delmarva (DMV1639) infectious bronchitis virus infection alters the microbiome of gastrointestinal and respiratory tracts of broiler chickens

Infectious bronchitis virus (IBV) is known to cause significant alterations in tracheal microbial flora in broiler chickens 5 days post-infection (dpi) and our focus is to understand the changes in both respiratory and gastrointestinal microbiome in broilers over a period of time following IBV infection. A study was conducted to characterize the tracheal and cecal microbiome in IBV infected and control broiler chickens at 6, 9 and 15 dpi. IBV genome in trachea, lung and cecal tonsils could be observed in the infected group at all the time points. Immune response parameters and histopathological lesion scores were significantly higher in IBV infected trachea and cecal tonsils at 6, 9 and 15 dpi compared to the controls. We observed that cecal microbial diversity (alpha diversity) was increased in the IBV infected group at 6 and 15 dpi. On the other hand, diversity (alpha diversity) of tracheal microbiome was elevated only at 9 dpi in the IBV infected group. Moreover, significant shift of microbial communities (beta diversity), in both cecum and trachea was observed following IBV infection. Enzyme and metabolic pathway analyses of cecum indicated an upregulation of DNA replication and cell wall synthesis pathways and a downregulation of pathways related to short chain fatty acid (SCFA) production in the IBV infected group compared to the controls. Analysis of tracheal metabolic pathways suggested initial adaptation to the infection stress and gradually shifting to enhanced microbial growth and stability. The study outcome adds to the understanding of microbiome changes secondary to histological changes and immune response following IBV infection in broiler chickens.

Exploration and application of microorganisms related to the inference of the time since deposition (TsD) in semen and blood stains

Determining the time since deposition (TsD) of body fluid stains can provide crucial criminal information to forensic researchers. Although there are studies on inferring residual time through DNA and RNA markers, this requires high sample quality, and microorganisms, as a new type of marker with individual and tissue identification capabilities, have the potential for body fluid recognition and TsD inference. Blood and semen are the most common types of bodily fluid stains at crime scenes, but research on the inference of the TsD of these two types of stains through microorganisms still needs to be explored. Thus, this study collected samples of body fluid stains exposed indoors for up to 56 days and selected several microorganisms that were both liquid specific and related to residual time inference in blood (Methylobacterium and Sphingomonas) and semen (Gardnerella) stains via 16 S rRNA high-throughput sequencing. Furthermore, the microorganisms' ability to infer TsD was verified using qPCR in validation group samples stored under the same conditions, and two multiple logistic regression models were constructed. The average absolute deviation of differences between the predicted and actual retention times of the three types of body fluids in the test set using two estimation methods was 2.15 and 2.06 days, respectively. In conclusion, this study has discovered four novel microorganisms related to the retention time of blood and semen and has preliminarily constructed the TsD prediction models, providing a new direction for future forensic research on the inference of TsD in blood and semen stains.

Growth performance and gut health of nursery pigs fed diet containing sodium butyrate or enzymatically hydrolyzed yeast product

Weaned pigs are highly susceptible to gut infections, underscoring the need to develop feeding strategies to manage gut health. A study was conducted to determine the effects of lipid-coated sodium butyrate (NaB) and enzymatically hydrolyzed yeast cell wall product (EYP) on growth performance and indicators of intestinal structure and function in nursery pigs. A total of 96 weaned pigs (initial BW = 6.60 ± 0.88 kg) housed in 24 pens (four pigs/pen) were fed three diets in a randomized complete block design. The diets were corn-soybean meal-based without (CON) or with 0.05% NaB or 0.1% EYP. Growth performance and fecal score were determined by the feeding phase. During days 10-13, one pig from each pen was euthanized for measuring organ weights, blood immune response, histology and permeability of small intestine, electrophysiological parameters of jejunum mounted in Ussing chambers, and gut microbiome. Dietary NaB, but not EYP, increased (P < 0.05) overall gain-to-feed ratio by 16%. In comparison to CON, dietary EYP increased (P < 0.05) the cecum weight by 36%, and dietary NaB or EYP tended to increase (P < 0.10) the villous height to crypt depth ratio in duodenum by 12%. Dietary NaB or EYP had no influence on the serum concentrations of immunoglobulins A, G, M, and tumor-necrosis factor-α. Dietary NaB decreased (P < 0.05) the jejunal flux of fluorescein isothiocyanate-dextran flux by 32%, whereas dietary EYP tended to reduce (P = 0.10) it by 21% compared to CON. Also, dietary Nab and EYP decreased (P < 0.05) jejunal short circuit current by 52 and 50%, respectively, compared to CON. Dietary EYP increased (P < 0.05) the relative abundance of Sporobacter and Desulfovibrio genera in the cecum. Dietary EYP increased (P < 0.05) the relative abundance of Verrucomicrobia phylum and Odoribacter, Enterococcus, and YRC22 genera in feces. In conclusion, dietary NaB improved feed efficiency and reduced jejunal permeability to fluorescein isothiocyanate-dextran 4 kDa, implying that it improved intestinal integrity in nursery pigs. Thus, NaB product fed in the current study can be included in diets for weaned pigs to improve their performance through improved gut integrity. Dietary EYP increased cecum weight, implying that dietary EYP improved cecal fermentation capacity. It also modified cecal and fecal microbial composition. Thus, the EYP product fed in the current study can be added in diets for weaned pigs to improve the fermentation of feed in the hindgut.

Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals

Colorectal polyps serve as the primary precursors for colorectal cancer. A close relationship has been observed between colorectal polyps and gut microbiota. However, the composition and role of the microbiome associated with tubular adenoma are not well understood. In this study, we prospectively evaluated alterations in gut microbiota among patients with colorectal polyps. A total of 60 subjects were enrolled in this study, including 30 patients with colorectal polyps (CP group) and 30 healthy controls (control group). The 16S rRNA sequencing was employed to characterize the gut microbiome in fecal samples. The results revealed that the beta diversity of the gut microbiota in the CP group significantly differs from that of the control group (p = 0.001). At the phylum level, the relative abundance of Bacteroides, Fusobacteria, and Proteobacteria was higher in the CP group compared to the control group (p < 0.05), whereas the relative abundance of Actinobacteria was higher in the control group in comparison to the CP group (p < 0.05). At the genus level, the abundance of Bacteroides increased in the CP group (p < 0.05), while Bifidobacterium declined in the CP group (p < 0.05). At the species level, the abundance of Clostridium perfringens, unidentified_Bacteroides, unidentified_Dorea, Escherichia coli, Clostridium ramosum, and Ruminococcus gnavus was higher (p < 0.05), whereas the abundance of Bifidobacterium adolescentis, unclassified_Bifidobacterium, Bifidobacterium longum, Faecalibacterium prausnitzii, and unidentified_Bifidobacterium is lower in CP group compared to the control group (p < 0.05). There was a structural imbalance in the composition of intestinal colonization flora for CP patients, characterized by a decrease in beneficial bacteria and an increase in harmful bacteria. Escherichia, Shigella, and Bacteroides may serve as promising biomarkers for early detection of colorectal polyps.

Analysis of microbial environment changes in wound healing of pressure ulcers in rats promoted by moist exposed burn ointment

This study explored the effects of Moist Exposed Burn Ointment (MEBO) on the healing process of pressure-induced wounds. Using a stage IV pressure ulcer model established in 42 rats, divided equally into a control gel group and an MEBO group, we investigated the efficacy of MEBO through topical application. The control group received Carbomer gel, while the MEBO group was treated with MEBO until complete wound healing. Results showed that MEBO significantly accelerated wound healing compared to the control group. Histological analysis, including hematoxylin and eosin (HE) staining and Masson's trichrome staining, revealed enhanced epithelialization and collagen deposition in the MEBO group. Furthermore, 16S rRNA sequencing indicated that MEBO reduced microbial diversity at the wound site and reshaped the microbial composition. Notably, The increased abundance of Acinetobacter and Staphylococcus, coupled with a reduction in Pseudomonas, may reflect a shift in the wound microbiome that could be conducive to healing. However, the exact role of these microbial shifts in promoting wound healing requires further investigation, as microbial dynamics in wound environments are complex and context-dependent. These findings suggest that MEBO facilitates wound healing by optimizing the wound microbiome, thereby offering a promising therapeutic approach for managing pressure ulcers.

Effects of Live and Peptide-Based Antimicrobiota Vaccines on Ixodes ricinus Fitness, Microbiota, and Acquisition of Tick-Borne Pathogens

This study explored the effects of antimicrobiota vaccines on the acquisition of Borrelia and Rickettsia, and on the microbiota composition of Ixodes ricinus ticks. Using a murine model, we investigated the immunological responses to live Staphylococcus epidermidis and multi-antigenic peptide (MAP) vaccines. Immunized mice were infected with either Borrelia afzelii or Rickettsia helvetica, and subsequently infested with pathogen-free I. ricinus nymphs. We monitored the tick feeding behavior, survival rates, and infection levels. Additionally, we employed comprehensive microbiota analyses, including the alpha and beta diversity assessments and microbial co-occurrence network construction. Our results indicate that both live S. epidermidis and MAP vaccines elicited significant antibody responses in mice, with notable bactericidal effects against S. epidermidis. The vaccination altered the feeding patterns and fitness of the ticks, with the Live vaccine group showing a higher weight and faster feeding time. Microbiota analysis revealed significant shifts in the beta diversity between vaccine groups, with distinct microbial networks and taxa abundances observed. Notably, the MAP vaccine group exhibited a more robust and complex network structure, while the Live vaccine group demonstrated resilience to microbial perturbations. However, the effects of antimicrobiota vaccination on Borrelia acquisition appeared taxon-dependent, as inferred from our results and previous findings on microbiota-driven pathogen refractoriness. Staphylococcus-based vaccines altered the microbiota composition but had no effect on B. afzelii infection, and yielded inconclusive results for R. helvetica. In contrast, previous studies suggest that E. coli-based microbiota modulation can induce a pathogen-refractory state, highlighting the importance of both bacterial species and peptide selection in shaping microbiota-driven pathogen susceptibility. However, a direct comparison under identical experimental conditions across multiple taxa is required to confirm this taxon-specific effect. These findings suggest that antimicrobiota vaccination influences tick fitness and microbiota assembly, but its effects on pathogen transmission depend on the bacterial taxon targeted and the selected peptide epitopes. This research provides insights into the need for strategic bacterial taxon selection to enhance vaccine efficacy in controlling tick-borne diseases.

Benefits of equilibrium between microbiota- and host-derived ligands of the aryl hydrocarbon receptor after stroke in aged male mice

Recent studies have highlighted the crucial role of microglia (MG) and their interactions with the gut microbiome in post-stroke neuroinflammation. The activation of immunoregulatory pathways, including the aryl hydrocarbon receptor (AHR) pathway, is influenced by a dynamic balance of ligands derived from both the host and microbiota. This study aimed to investigate the association between stroke-induced dysbiosis and the resultant imbalance in AHR ligand sources (loss of microbiota-derived [indole-based] and increase of host-derived [kynurenine-based]) after stroke. Microbiota-derived AHR ligands decreased in human plasma and remained low for days following an ischemic stroke highlighting the translational significance. Transient-middle-cerebral-artery-occlusion was performed in aged wild-type and germ-free male mice. MG-AHR expression and activity increased in both in vivo and ex vivo stroke models. Germ-free mice showed altered neuroinflammation and antigen presentation while aged mice showed reduced infarct volume and neurological deficits following treatment with microbiota-derived AHR ligands after stroke. Restoring a balanced pool of host- and microbiota-derived AHR ligands may be beneficial after stroke and may represent a therapeutic target.

Escherichia Abundance and Metabolism Align with Vitiligo Disease Activity

Vitiligo is a cutaneous autoimmune disorder characterized by progressive depigmentation due to melanocyte destruction by cytotoxic T cells. Genetic factors predispose patients to the disease and are supported by environmental factors that often initiate new disease episodes. We investigated whether disease outcomes were partially defined by pathogenic microbes that drive nutrient deficiency and inflammation. Our study presents the results of research on the diet and gut microbiome composition of patients with vitiligo and healthy controls from Kazakhstan and the United States. Dietary nutrient intake was assessed using the National Institutes of Health-generated Diet History Questionnaire. Patients with active vitiligo exhibit a limited intake of specific fatty acids, amino acids, fiber, and zinc. Disease activity was further characterized by the abundance of Odoribacter and Escherichia in the gut. Metabolic pathway analysis supported the role of the Escherichia genus in disease activity by limiting energy metabolism and amino acid biosynthetic pathways. Disease activity also aligned with elevated circulating pro-inflammatory cytokines. These findings suggest that nutritional limitations are not compensated by metabolites from the gut microbiome in active disease, potentially leaving room for inflammation and exacerbating vitiligo. The intricate relationship among diet, gut microbiome composition, and disease progression in vitiligo highlights potential avenues for targeted interventions to reduce autoimmune activity and improve patient outcomes.

Nasal pathobiont abundance does not differ between dairy cattle with or without clinical symptoms of bovine respiratory disease

BACKGROUND

Bovine respiratory disease (BRD) remains a significant health and economic problem to the dairy cattle industry. Multiple risk factors contribute to BRD susceptibility including the bacterial pathobionts Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Studies have characterized and quantified the abundance of these bacteria in the nasal cavity of cattle to infer and help disease diagnosis; nonetheless, there is still discrepancy in the results observed of when these microbes are commensal or pathogenic. Additionally, some of these studies are limited to a specific farm. The goal of this study is to compare the nasal microbiome community (diversity and composition) and the abundance of the four bacterial pathogens (by qPCR) in the nasal cavity to identify differences between dairy calves that are apparently healthy and those identified to have BRD. Nasal swabs were collected from approximately 50 apparently healthy and 50 BRD-affected calves sampled from five different dairy farms in the US (CA, IN, NY (two farms), and TX).

RESULTS

Calves diagnosed with BRD in NY, and TX had lower nasal microbiome diversity compared to the apparently healthy calves. Differences in the nasal microbiome composition were observed between the different farms predicted by Bray-Curtis and weighted UniFrac dissimilarities. Commensal and pathobiont genera Acinetobacter, Moraxella, Psychrobacter, Histophilus, Mannheimia, Mycoplasma, and Pasteurella were prevalent in the bovine nasal microbiome regardless of farm or disease status. The BRD-pathobiont H. somni was the most prevalent pathobiont among all the samples and M. bovis the least prevalent. Only in CA was the abundance of a pathobiont different according to disease status, where M. haemolytica was significantly more abundant in the BRD-affected animals than apparently healthy animals.

CONCLUSIONS

This study offers insight into the nasal microbiome community composition in both animals diagnosed with BRD and healthy animals, and shows that the farm effect plays a more significant role in determining the microbiome community than disease status in young dairy calves.

Systematic analyses uncover robust salivary microbial signatures and host-microbiome perturbations in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is a prevalent malignancy in the oral-maxillofacial region with a poor prognosis. Oral microbiomes play a potential role in the pathogenesis of this disease. However, findings from individual studies have been inconsistent, and a comprehensive understanding of OSCC-associated microbiome dysbiosis remains elusive. Here, we conducted a large-scale meta-analysis by integrating 11 publicly available data sets comprising salivary microbiome profiles of OSCC patients and healthy controls. After correcting for batch effects, we observed significantly elevated alpha diversity and distinct beta-diversity patterns in the OSCC salivary microbiome compared to healthy controls. Leveraging random effects models, we identified robust microbial signatures associated with OSCC across data sets, including enrichment of taxa such as Streptococcus, Lactobacillus, Prevotella, Bulleidia moorei, and Haemophilus in OSCC samples. The machine learning models constructed from these microbial markers accurately predicted OSCC status, highlighting their potential as non-invasive diagnostic biomarkers. Intriguingly, our analyses revealed that the age- and gender-associated signatures in normal saliva microbiome were disrupted in the OSCC, suggesting perturbations in the intricate host-microbe interactions. Collectively, our findings uncovered complex alterations in the oral microbiome in OSCC, providing novel insights into disease etiology and paving the way for microbiome-based diagnostic and therapeutic strategies. Given that the salivary microbiome can reflect the overall health status of the host and that saliva sampling is a safe, non-invasive approach, it may be worthwhile to conduct broader screening of the salivary microbiome in high-risk OSCC populations as implications for early detection.

IMPORTANCE

The oral cavity hosts a diverse microbial community that plays a crucial role in systemic and oral health. Accumulated research has investigated significant differences in the saliva microbiota associated with oral cancer, suggesting that microbiome dysbiosis may contribute to the pathogenesis of oral squamous cell carcinoma (OSCC). However, the specific microbial alterations linked to OSCC remain controversial. This meta-analysis reveals robust salivary microbiome alterations. Machine learning models using differential operational taxonomic units accurately predicted OSCC status, highlighting the potential of the salivary microbiome as a non-invasive diagnostic biomarker. Interestingly, age- and gender-associated signatures in the normal salivary microbiome were disrupted in OSCC, suggesting perturbations in host-microbe interactions.

Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition

Microbiome analysis has become a crucial tool for basic and translational research due to its potential for translation into clinical practice. However, there is ongoing controversy regarding the comparability of different bioinformatic analysis platforms and a lack of recognized standards, which might have an impact on the translational potential of results. This study investigates how the performance of different microbiome analysis platforms impacts the final results of mucosal microbiome signatures. Across five independent research groups, we compared three distinct and frequently used microbiome analysis bioinformatic packages (DADA2, MOTHUR, and QIIME2) on the same subset of fastQ files. The source data set encompassed 16S rRNA gene raw sequencing data (V1-V2) from gastric biopsy samples of clinically well-defined gastric cancer (GC) patients (n = 40; with and without Helicobacter pylori [H. pylori] infection) and controls (n = 39, with and without H. pylori infection). Independent of the applied protocol, H. pylori status, microbial diversity and relative bacterial abundance were reproducible across all platforms, although differences in performance were detected. Furthermore, alignment of the filtered sequences to the old and new taxonomic databases (i.e., Ribosomal Database Project, Greengenes, and SILVA) had only a limited impact on the taxonomic assignment and thus on global analytical outcomes. Taken together, our results clearly demonstrate that different microbiome analysis approaches from independent expert groups generate comparable results when applied to the same data set. This is crucial for interpreting respective studies and underscores the broader applicability of microbiome analysis in clinical research, provided that robust pipelines are utilized and thoroughly documented to ensure reproducibility.IMPORTANCEMicrobiome analysis is one of the most important tools for basic and translational research due to its potential for translation into clinical practice. However, there is an ongoing controversy about the comparability of different bioinformatic analysis platforms and a lack of recognized standards. In this study, we investigate how the performance of different microbiome analysis platforms affects the final results of mucosal microbiome signatures. Five independent research groups used three different and commonly used bioinformatics packages for microbiome analysis on the same data set and compared the results. This data set included microbiome sequencing data from gastric biopsy samples of GC patients. Regardless of the protocol used, Helicobacter pylori status, microbial diversity, and relative bacterial abundance were reproducible across all platforms. The results show that different microbiome analysis approaches provide comparable results. This is crucial for the interpretation of corresponding studies and underlines the broader applicability of microbiome analysis.

The Gut Microbiota Metabolite Butyrate Modulates Acute Stress-Induced Ferroptosis in the Prefrontal Cortex via the Gut-Brain Axis

Stress has been implicated in the onset of mental disorders such as depression, with the prefrontal cortex (PFC) playing a crucial role. However, the underlying mechanisms remain to be fully elucidated. Metabolites secreted by intestinal flora can enter the bloodstream and exert regulatory effects on the body. Consequently, this study aims to investigate the molecular mechanisms by which gut flora influences ferroptosis in PFC neurons, thereby affecting depression-like behavioral changes in mice subjected to acute stress. Initially, we established a mouse model of acute restraint stress (3-day duration) and verified that stress-induced ferroptosis of PFC neurons contributed to depression-like behavioral alterations in mice, as evidenced by morphological, behavioral, and molecular biology assessments. Subsequently, through fecal microbiota transplantation (FMT) experiments, we established a significant correlation between gut microbiota and ferroptosis of PFC neurons in acute stress-exposed mice. 16S rDNA sequencing identified butyric acid-producing bacteria, specifically g_Butyricimonas and its primary metabolite, butyric acid, as critical regulators of ferroptosis in PFC neurons in acutely stressed mice. Furthermore, the intervention of butyrate demonstrated its potential to ameliorate damage to the intestinal and blood-brain barriers in these mice. This intervention also mitigated depression-like behaviors induced by ferroptosis of PFC neurons by alleviating systemic inflammatory responses. The findings of this study indicate that acute stress-induced ferroptosis of PFC neurons plays a critical role in depression-like behavioral changes in mice. Additionally, the gut microbiota metabolite butyrate can modulate ferroptosis and depression-like behavioral changes through the gut-brain axis.

Long-term and seasonal evaluation on environmental microbiology and water quality of Shanmei reservoir in southeast China

As a crucial source of potable water, the quality of water in Shanmei reservoir strongly and directly impacts the safety and well-being of downstream residents. Microorganisms play a pivotal role in the reservoir's resource and energy cycle. However, ecological protection efforts for the Shanmei reservoir have encountered numerous challenges in recent years. This study conducted an extensive visual analysis of microbial communities in sediment from the Shanmei reservoir between 2022 and 2024 using amplicon sequencing technology targeting 16S rRNA gene. The results showed that the microbial diversity of sediment showed an obvious seasonal pattern. At the same time, microbial composition also changes with the long-term evolution of time, which may be closely related to the change in environmental conditions. In addition, we have also carried out long-term multi-dimensional monitoring of the water quality of the Shanmei reservoir, and the results show that the water quality has reached the national drinking water grade. In conclusion, this study not only unveiled the interseasonal dynamics and long-term evolutionary characteristics of sediment microbial communities but also elucidated the significant influence of environmental factors on their composition, structure and function. These findings offer a fresh perspective for understanding the freshwater ecosystem microbial dynamics and provide a scientific foundation for reservoir management and water quality protection.

Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience

The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.

Effects of Monascus pilosus SWM 008-Fermented Red Mold Rice and Its Functional Components on Gut Microbiota and Metabolic Health in Rats

Red mold rice, fermented by Monascus spp., has been reported to modulate gut microbiota composition and improve metabolic health. Previous studies indicate that red mold rice can reduce cholesterol, inhibit hepatic lipid accumulation, and enhance bile acid excretion, while also altering gut microbiota under high-fat dietary conditions. However, it remains unclear whether these effects are directly due to Monascus-derived products modulating gut microbiota or are a consequence of improved metabolic health conditions, which indirectly influence gut microbiota. This study aimed to evaluate the effects of Monascus pilosus SWM 008 fermented red mold rice and its components-monascin, monascinol, ankaflavin, and polysaccharides-on gut microbiota and metabolic health in rats fed a normal diet. Over eight weeks, physiological, biochemical, and gut microbiota parameters were assessed. Results showed no significant changes in body weight or liver/kidney function, confirming safety. Gut microbiota analysis revealed that red mold rice, monascin, monascinol, and polysaccharides significantly altered gut microbiota composition by increasing the relative abundance of beneficial bacteria, such as Akkermansia muciniphila, Ligilactobacillus murinus, and Duncaniella dubosii. Functional predictions indicated enhanced vitamin K2 biosynthesis, nucleotide metabolism, and other metabolic pathways linked to improved gut health. In conclusion, Monascus pilosus SWM 008 fermented red mold rice demonstrated safety and beneficial effects, suggesting its potential as a functional food to maintain gut microbiota balance under normal dietary conditions.

Microbial community analysis of sand filters used to treat mine water from a closed uranium mine

Rapid sand filters (RSFs) are employed in a drinking water treatment to remove undesirable elements such as suspended solids and dissolved metal ions. At a closed uranium (U) mine site, two sets of tandemly linked paired RSF systems (RSF1-RSF2 and RSF1-RSF3) were utilized to remove iron and manganese from mine water. In this study, a 16S rRNA-based amplicon sequencing survey was conducted to investigate the core microbes within the RSF system treating the mine water. In RSF1, two operational taxonomic units (OTUs) related to methanotrophic bacteria, Methylobacter tundripaludum (relative abundance: 18.1%) and Methylovulum psychrotolerans (11.5%), were the most and second most dominant species, respectively, alongside iron-oxidizing bacteria. The presence of these OTUs in RSF1 can be attributed to the microbial community in the inlet mine water, as the three most abundant OTUs in the mine water also dominated RSF1. Conversely, in both RSF2 and RSF3, Nevskia sp., previously isolated from the Ytterby mine manganese oxide producing ecosystem, became dominant, although known manganese-oxidizing bacterial OTUs were not detected. In contrast, a unique OTU related to Rhodanobacter sp. was the third most abundant (8.0%) in RSF1, possibly due to selective pressure from the radionuclide-contaminated environment during RSF operation, as this genus is known to be abundant at nuclear legacy waste sites. Understanding the key bacterial taxa in RSF system for mine water treatment could enhance the effectiveness of RSF processes in treating mine water from closed U mines.

The gastric microbiome altered by A4GNT deficiency in mice

Background

Selective antimicrobial effects have been found for α1,4-linked N-acetylglucosamine residues at the terminus of O-glycans attached to a core protein of gastric gland mucin. A4gnt encodes α1,4-N-acetylglucosaminyl transferase, which is responsible for the biosynthesis of α1,4-linked N-acetylglucosamine. The impact of A4GNT on the establishment and homeostasis of the gastric microbiome remains to be clarified. The aim of this study was to characterize the gastric microbiome in mice deficient for the production of α1,4-linked N-acetylglucosamine.

Methods

The gastric microbiome within A4gnt -/- mice and wild-type mice was analyzed using high-throughput sequencing of bacterial 16S rRNA.

Results

In A4gnt -/- mice, which spontaneously develop gastric cancer, the community structure of the gastric microbiome was altered. The relative abundance of mutagenic Desulfovibrio and proinflammatory Prevotellamassilia in these mice was significantly increased, especially 4 weeks after birth. The co-occurrence network appeared to be much more complex. Functional prediction demonstrated considerable decreases in the relative frequencies of functions associated with polysaccharide metabolism and transportation.

Conclusion

The distinct profile in A4gnt -/- mice demonstrated a vital role of A4GNT in the establishment of the gastric microbiome. A dysbiotic gastric microbiome may contribute to the spontaneous development of gastric cancer in mice.

Microbial community variations in adult Hyalomma dromedarii ticks from single locations in Saudi Arabia and Tunisia

Introduction

The camel-infesting tick, Hyalomma dromedarii, is a prominent ectoparasite in the Middle East and North Africa (MENA) region, critically impacting camel health and acting as a vector for tick-borne pathogens. Despite prior studies on its microbiota, the effects of geographic origin and sex on microbial community structure and functional stability remain poorly understood.

Methods

To address this, we characterized the bacterial microbiota of H. dromedarii ticks collected from camels in Tunisia (TUN) and Saudi Arabia (SA) using 16S rRNA gene sequencing, microbial network analysis, and metabolic pathway prediction.

Results

Our findings indicate a dominant presence of Francisella endosymbionts in Tunisian ticks, suggesting adaptive roles of H. dromedarii ticks in arid ecosystems. Keystone taxa, particularly Staphylococcus and Corynebacterium, were identified as central to microbial network structure and resilience. Moreover, network robustness analyses demonstrated enhanced ecological stability in the Tunisian tick microbiota under perturbation, indicative of higher resilience to environmental fluctuations compared to Saudi Arabian ticks. Additionally, functional pathway predictions further revealed geographically distinct metabolic profiles between both groups (Tunisia vs. Saudi Arabia and males vs. females), underscoring environmental and biological influences on H. dromedarii microbiota assembly.

Discussion

These results highlight region-specific and sex-specific microbial adaptations in H. dromedarii, with potential implications for pathogen transmission dynamics and vector resilience. Understanding these microbial interactions may contribute to improved strategies for tick control and tick-borne disease prevention.

phylotypr: an R package for classifying DNA sequences

The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.

A Comprehensive Dataset on Microbiome Dynamics in Rheumatoid Arthritis from a Large-Scale Cohort Study

Alterations in intestinal microbiota have been identified as a key risk factor in rheumatoid arthritis (RA). This study presents a multidimensional gut microbiota profile from a large cohort of RA patients, stratified by disease stage and treatment regimens, and compared to healthy controls. Our dataset comprises gut microbiota profiles from 2,238 individuals, including 1,034 RA patients (Ascia Pacific RA cohort, APRAC) and 1,204 healthy controls. This dataset is enriched with detailed clinical metadata, including patient profiles, treatment histories, and environmental factors, providing a comprehensive "disease exposome" for RA. By integrating 16S rRNA gene sequencing with demographic, clinical, and environmental data, we offer a valuable resource to explore the complex relationships between gut microbiota and RA progression. This large-scale dataset is expected to be a foundation for collaborative research, advancing our understanding of the microbiome's systemic effects in RA and other autoimmune diseases and potentially guiding new therapeutic approaches.

MultiTax-human: an extensive and high-resolution human-related full-length 16S rRNA reference database and taxonomy

Considering that the human microbiota plays a critical role in health and disease, an accurate and high-resolution taxonomic classification is thus essential for meaningful microbiome analysis. In this study, we developed an automatic system, named MultiTax pipeline, for generating de novo taxonomy from full-length 16S rRNA sequences using the Genome Taxonomy Database and other existing reference databases. We first constructed the MultiTax-human database, a high-resolution resource specifically designed for human microbiome research and clinical applications. The database includes 842,649 high-quality full-length 16S rRNA sequences, extracted from multiple public repositories and human-related studies, offering a comprehensive and accurate portrayal of the human microbiome. To validate the MultiTax-human database, we profiled the human microbiome across various body sites, identified core microbial taxa, and tested its performance using an independent data set. Additionally, the database is equipped with a user-friendly web interface for easy querying and data exploration. The MultiTax-human database is poised to serve as a valuable tool for researchers, enhancing the precision of human microbiome studies and advancing our understanding of its impact on human health and diseases.IMPORTANCEUnderstanding the human microbiome, the collection of microorganisms in and on our bodies, is essential for advancing health research. Current methods often lack precision and consistency, hindering our ability to study these microorganisms effectively. Our study presents the MultiTax-human database, a high-resolution reference tool specifically designed for human microbiome research. By integrating data from multiple sources and employing advanced classification techniques, this database offers an accurate and detailed map of the human microbiome. This resource enhances the ability of researchers and clinicians to explore the roles of microorganisms in health and disease, potentially leading to improved diagnostics, treatments, and insights into various medical conditions.

Disruption of Gut Microbiota and Associated Fecal Metabolites in Collagen-Induced Arthritis Mice During the Early Stage

Background

Rheumatoid arthritis (RA) is a chronic autoimmune disease and increasing evidence suggests that disturbances in the composition and function of gut microbiota are potentially implicated in the progression of RA. Further revealing the microbiota and related metabolic disorders in the preclinical stage of RA (pre-RA) is of great significance for exploration of disease mechanisms.

Methods

DBA/1 mice were injected with type II collagen on days 0 and 21 to establish collagen-induced arthritis (CIA) mouse model. Footpad thickness, serum autoantibodies, and joint histopathology were used to assess the progression of RA. A combination of 16S rRNA sequencing, untargeted metabolomics and targeted short-chain fatty acids (SCFAs) analysis were employed to comprehensively investigate the alterations of gut microbiota and fecal metabolites in CIA during the pre-RA stage.

Results

20 days after the initial collagen immunization, CIA mice showed immune responses without joint symptoms, alongside gut microbiota disruption. Alterations were observed in 20 microbial taxa, including Oscillospira, Bifidobacterium, Ruminococcus, Allobaculum, Alistipes, Lactobacillus, and Candidatus_Arthromitus, etc. Untargeted and targeted metabolomics identified 33 altered fecal metabolites, mainly including sugars and their derivatives, amino acids, long-chain fatty acids and SCFAs, etc. Correlation analysis showed significant correlations between specific gut microbial abundances and fecal metabolite levels. Especially, SCFAs were strongly associated with Bifidobacterium, Alistipes, Ruminococcus, Anaerotruncus, and Allobaculum.

Conclusion

These findings suggest that collagen immunization leads to disruption of gut microbiome and induces changes of fecal metabolites in mice, which may play a key role in early development of RA in CIA mice.

Insight into the bacterial communities in the sediment-water interface across different salinities of Pacific White shrimp, Penaeus vannamei, by metabarcoding

Microbes play an important role in the food chain by metabolizing organic matter, cycling nutrients, and maintaining a dynamic equilibrium among organisms in water and sediment. The objective is to study the fluctuating taxonomic microbial diversity profile in the sediment-water interface at different days of culture (DOC) of Penaeus vannamei in varying salinities using the Illumina MiSeq platform. Sediment samples were collected in Tamil Nadu, India, from low-saline, brackish water, and high-saline ponds at 30, 60, and 90 DOC. Bacterial richness and diversity in species were high in low-saline ponds. Beta-diversity variation indicated more differences in bacterial composition in high- and low-saline ponds. The predominant phyla observed were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, and Cyanobacteria. High-saline ponds accounted for more nitrification bacterial communities, sulfur-reducing bacterial communities, sulfur-oxidizing bacterial communities, and high redox potential, whereas denitrification bacterial communities were high in brackish water ponds.

Bifidobacterium animalis ssp. lactis BX-245-fermented milk alleviates tumor burden in mice with colorectal cancer

Colorectal cancer (CRC) arises from the accumulation of abnormal mutations in colorectal cells during prolonged inflammation. This study aimed to investigate the potential of probiotic fermented milk containing the probiotic strain, Bifidobacterium animalis ssp. lactis BX-245 (BX-245), in alleviating tumor burden in CRC mice induced by azoxymethane and dextran sodium sulfate. The study monitored changes in tumor size and number, gut microbiota, metabolomics, and inflammation levels before and after the intervention. Our findings indicate that intragastric administration of BX245-fermented milk effectively modulated the intratumor microbiota, as well as the gut microbiota and its metabolism. We also observed a decreased relative abundance of intratumor Akkermansia in the CRC mice, while the intratumor Parabacteroides exhibited a significant positive correlation with tumor number and weight. Moreover, administering BX245-fermented milk significantly reduced gut barrier permeability, alleviated gut barrier damage, and increased serum IL-2 and IFN-γ levels compared with the ordinary fermented milk group. Collectively, our data suggest that administering probiotic fermented milk containing specific functional strains such as BX245 could result in a reduction in tumor burden in CRC mice. Conversely, ordinary fermented milk did not show the same tumor-inhibiting effects. The current results are preliminary, and further confirmation is necessary to establish the causal relationship among probiotic milk, changes in gut microbiota, and disease alleviation.

Linking dietary fiber to human malady through cumulative profiling of microbiota disturbance

Dietary fiber influences the composition and metabolic activity of microbial communities, impacting disease development. Current understanding of the intricate fiber-microbe-disease tripartite relationship remains fragmented and elusive, urging a systematic investigation. Here, we focused on microbiota disturbance as a robust index to mitigate various confounding factors and developed the Bio-taxonomic Hierarchy Weighted Aggregation (BHWA) algorithm to integrate multi-taxonomy microbiota disturbance data, thereby illuminating the complex relationships among dietary fiber, microbiota, and disease. By leveraging microbiota disturbance similarities, we (1) classified 32 types of dietary fibers into six functional subgroups, revealing correlations with fiber solubility; (2) established associations among 161 diseases, uncovering shared microbiota disturbance patterns that explain disease co-occurrence (e.g., type II diabetes and kidney diseases) and distinct microbiota patterns that discern symptomatically similar diseases (e.g., inflammatory bowel disease and irritable bowel syndrome); (3) designed a body-site-specific microbiota disturbance scoring scheme, computing a disturbance score (DS) for each disease and highlighting the pronounced capacity of Crohn's disease to disturb gut microbiota (DS = 14.01) in contrast with food allergy's minimal capacity (DS = 0.74); (4) identified 1659 fiber-disease associations, predicting the potential of dietary fiber to modulate specific microbiota changes associated with diseases of interest; (5) established murine models of inflammatory bowel disease to validate the preventive and therapeutic effects of arabinoxylan that notably perturbed the Bacteroidetes and Firmicutes phyla, as well as the Bacteroidetes and Lactobacillus genera, aligning with our model predictions. To enhance data accessibility and facilitate targeted dietary intervention development, we launched an interactive webtool-mDiFiBank at https://mdifibank.org.cn/.

Topology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults

Gut microbiota with co-abundant behaviors is considered belonging to the same guild in micro-ecosystem. In this study, we established co-abundance networks of operational taxonomic units (OTUs) among 2944 Chinese adults from the Shanghai Men's and Women's Health Studies and observed a positive connection-dominated scale-free network using Sparse Correlations for Compositional data (SparCC). The closeness centrality was negatively correlated with other degree-based topological metrics in the network, indicating the isolated modularization of the bacteria. A total of 130 guilds were constructed, with a high modularity of 0.68, and retaining more diversity of OTUs than genus classification. The scores of guild structure similarity for comparisons between all, the healthy and the unhealthy subjects were higher than those derived from randomized permutations, suggesting a robust guild structure. We further used the constructed 130 guilds as the aggregation units to identify gut microbiota that may be associated with type 2 diabetes, and found that the OTUs in 21 significant guilds relevant to diabetes belonged to 19 of 41 (46.3%) previously reported genera (derived from Disbiome database), while only 10 (24.4%) showed different abundances between diabetes patients and healthy subjects in genus-based analysis. Our study reveals modularization of gut microbiota as guilds in Chinese populations, and demonstrates advantages of guild-based analysis in identifying diabetes-related gut bacteria. The analytical method based on microbial networks should be widely used to deepen our understanding of the role of gut microbiota in human health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-024-00211-8.

Oral microbiota as a biomarker for predicting the risk of malignancy in indeterminate pulmonary nodules: a prospective multicenter study

BACKGROUND

Determining the benign or malignant status of indeterminate pulmonary nodules (IPN) with intermediate malignancy risk is a significant clinical challenge. Oral microbiota-lung cancer (LC) interactions have qualified oral microbiota as a promising non-invasive predictive biomarker in IPN.

MATERIALS AND METHODS

Prospectively collected saliva, throat swabs, and tongue coating samples from 1040 IPN patients and 70 healthy controls across three hospitals. Following up, the IPNs were diagnosed as benign (BPN) or malignant pulmonary nodules (MPN). Through 16S rRNA sequencing, bioinformatics analysis, fluorescence in situ hybridization (FISH), and seven machine learning algorithms (support vector machine, logistic regression, naïve Bayes, multi-layer perceptron, random forest, gradient-boosting decision tree, and LightGBM), we revealed the oral microbiota characteristics at different stages of HC-BPN-MPN, identified the sample types with the highest predictive potential, constructed and evaluated the optimal MPN prediction model for predictive efficacy, and determined microbial biomarkers. Additionally, based on the SHAP algorithm interpretation of the ML model's output, we have developed a visualized IPN risk prediction system on the web.

RESULTS

Saliva, tongue coating, and throat swab microbiotas exhibit site-specific characteristics, with saliva microbiota being the optimal sample type for disease prediction. The saliva-LightGBM model demonstrated the best predictive performance (AUC = 0.887, 95%CI: 0.865-0.918), and identified Actinomyces, Rothia, Streptococcus, Prevotella, Porphyromonas , and Veillonella as biomarkers for predicting MPN. FISH was used to confirm the presence of a microbiota within tumors, and external data from a LC cohort, along with three non-IPN disease cohorts, were employed to validate the specificity of the microbial biomarkers. Notably, coabundance analysis of the ecological network revealed that microbial biomarkers exhibit richer interspecies connections within the MPN, which may contribute to the pathogenesis of MPN.

CONCLUSION

This study presents a new predictive strategy for the clinic to determine MPNs from BPNs, which aids in the surgical decision-making for IPN.

Unveiling the P-solubilizing potential of bacteria enriched from natural colonies of Red Sea Trichodesmium spp

Phosphorus (P) is pivotal for all organisms, yet its availability is, particularly in the marine habitat, limited. Natural, puff-shaped colonies of Trichodesmium, a genus of diazotrophic cyanobacteria abundant in the Red Sea, have been demonstrated to capture and centre dust particles. While this particle mining strategy is considered to help evade nutrient limitation, details behind the mechanism remain elusive. This study explores P-solubilizing bacteria (PSB) residing within Trichodesmium's associated microbial community, their potential contribution to the host, and the possible implications for P cycling in marine ecosystems. Bacterial enrichment on YBCII medium resulted in 28 enrichment cultures, primarily comprising bacterial families such as Rhodobacteraceae, Alteromonadaceae and Burkholderiaceae. Five enrichment cultures were further grown on hydroxyapatite, revealing their ability to consume and release Nitrogen and P while forming strong physical interactions with the mineral. A drop in pH was observed, indicating acid production as the primary P-solubilizing pathway. Co-cultivation experiments confirmed a positive effect on Trichodesmium erythraeum strain IMS101 growth by the presence of putative PSBs. These results reveal that the enriched bacteria exhibit significant P-solubilizing activity, thus potentially increasing the bioavailability of P in seawater. Thus, PSB could play a vital role in maintaining the P balance in the Red Sea, supporting the growth of Trichodesmium spp. and other marine organisms. Overall, our results contribute to a deeper understanding of the P cycle in the Red Sea and have implications for developing novel strategies for P management in marine ecosystems.

The gut-liver axis links the associations between serum carotenoids and non-alcoholic fatty liver in a 7.8-year prospective study

Background

Many studies have shown that carotenoids are beneficial to non-alcoholic fatty liver disease (NAFLD). Therefore, we explored potential biomarkers of gut microbiota and fecal and serum metabolites linking the association between serum carotenoids and NAFLD in adults.

Methods

This 7.8-year prospective study included 2921 participants with serum carotenoids at baseline and determined NAFLD by ultrasonography (ULS-NAFLD) every 3 years. A total of 828 subjects additionally underwent magnetic resonance imaging to identify NAFLD (MRI-NAFLD). Gut microbiota was analyzed by 16S rRNA sequencing in 1,661 participants, and targeted metabolomics profiling in 893 feces and 896 serum samples was performed by ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) in the middle term.

Results

A total of 2,522 participants finished follow-up visits. Of these participants, 770, 301, 474, and 977 were categorized into NAFLD-free, improved, new-onset, and persistent NAFLD groups based on their ULS-NAFLD status changes, respectively, and 342/828 were MRI-verified NALFD. Longitudinal analyses showed an inverse association between carotenoids and NALFD risk/presence (P-trend <0.05). Multivariable-adjusted odds ratios (ORs)/hazard ratio (HR) [95% confidence intervals (CIs)] of NAFLD for quartile 4 (vs. quartile 1) of total carotenoids were 0.63 (0.50, 0.80) for incident ULS-NAFLD, 0.20 (0.15, 0.27) for persistent ULS-NAFLD, 1.53 (1.10, 2.12) for improved-NAFLD, and 0.58 (0.39, 0.87) for MRI-NAFLD. The biomarkers in the gut-liver axis significantly associated with both serum carotenoids and NAFLD included sixteen microbial genera mainly in Ruminococcaceae and Veillonellaceae family, nineteen fecal metabolites containing medium-chain fatty acids (MCFAs), bile acids, and carnitines, and sixteen serum metabolites belonging to organic acids and amino acids. The total carotenoids-related scores of significant microbial genera, fecal and serum metabolites mediated the carotenoids-NAFLD association by 8.72%, 12.30%, and 16.83% (all P<0.05) for persistent NAFLD and 9.46%, 8.74%, and 15.7% for incident-NAFLD, respectively.

Conclusions

Our study reveals a beneficial association of serum carotenoids and incident and persistent NAFLD. The identified gut-liver axis biomarkers provided mechanistic linkage for the epidemiological association.

Bovine colostrum prevents formula-induced gut microbiota dysbiosis in preterm pigs

BACKGROUND

Preterm birth and formula feeding increase the risk of necrotizing enterocolitis (NEC), a gut inflammatory disease known to be associated with gut microbiota (GM) changes in infants. Supplemental bovine colostrum may protect against formula-induced NEC via GM changes. We hypothesised that feeding colostrum before, after, or during formula feeding affects NEC sensitivity via changes to GM.

METHODS

Colonic GM (profiled by 16S ribosomal RNA gene amplicon sequencing) was compared in preterm pigs fed colostrum for 4 days, either before, after, or together with formula feeding for 4 days. Correlations between GM and gut parameters were assessed on day 5 or 9.

RESULTS

Both exclusive and partial colostrum feeding induced higher GM diversity, lower Enterococcus abundance, and improved intestinal maturation parameters (villus structure, digestive enzyme activities, permeability), relative to exclusive formula feeding (all p < 0.05). Across feeding regimens, Enterococcus abundance was inversely correlated with intestinal maturation parameters. Conversely, there was no correlation between GM changes and early NEC lesions.

CONCLUSION

Bovine colostrum inhibits formula-induced Enterococcus overgrowth and gut dysfunctions just after preterm birth but these effects are not causally linked. Optimising diet-related host responses, not GM, may be critical to prevent NEC in preterm newborn pigs and infants.

IMPACT

Supplement of bovine colostrum to formula feeding modified the gut microbiota by increasing species diversity and reducing Enterococcus abundance, while concurrently improving intestinal functions in preterm pigs. Diet-related changes to the gut microbiota were not clearly associated with development of necrotizing enterocolitis (NEC) in preterm pigs, suggesting that diet-related gut microbiota effects are not critical for diet-related NEC protection. The study highlights the potential to use bovine colostrum as a supplement to formula feeding for preterm infants lacking human milk.

Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study

OBJECTIVE

To identify a microbial signature for endometriosis for use as a diagnostic non-invasive biomarker.

DESIGN

Prospective cohort pilot study.

SETTING

Nepean Hospital and UNSW Microbiome Research Centre, Australia.

POPULATION

Sixty-four age- and sex-matched subjects (n = 19 healthy control (HC); n = 24 non-endometriosis (N-ENDO) and n = 21 confirmed endometriosis (ENDO)). All study participants, besides healthy controls, underwent laparoscopic surgical assessment for endometriosis, and histology was performed on excised lesions.

METHODS

Oral, stool and, vaginal samples were self-collected at a single time point for healthy controls, and preoperatively for patients undergoing laparoscopy. Samples underwent 16S rRNA amplicon sequencing, followed by bioinformatics analysis.

MAIN OUTCOME MEASURES

Compositional differences between cohorts as identified by diversity analyses, and differentially abundant microbial taxa, as identified by LEfSE analysis.

RESULTS

The composition of the oral (adjusted p = 0.003), and stool (adjusted p = 0.042) microbiota is different between the three cohorts. Differentially abundant taxa are present within each cohort as identified by LEfSE analysis. Particularly, Fusobacterium was enriched in the oral samples of patients with moderate/severe endometriosis.

CONCLUSIONS

Taxonomic and compositional differences were found between the microbiota in the mouth, gut and, vagina of patients with and without endometriosis and healthy controls. Fusobacterium was enriched in patients with moderate/severe endometriosis. Fusobacterium is noted as a key pathogen in periodontal disease, a common comorbidity in endometriosis. These findings suggest a role for the oral, stool and, vaginal microbiome in endometriosis, and present potential for microbial-based treatments and the design of a diagnostic swab.

Isolated White Lupin Proteins Beneficially Modulate the Intestinal Microbiota Composition in Rats

BACKGROUND

Previous work has shown that the mostly beneficial modulation of intestinal microbiota generally found with legume-based diets is likely to be due, at least in part, to their constituent protein components.

OBJECTIVES

The faecal microbiota composition was studied in rats fed diets differing only in their constituent proteins.

METHODS

Rats (n = 10/group) were fed for 28 days diets based in milk [(lactalbumin (LA), casein (CAS)], or white lupin (Lupinus albus) protein isolate (LPI).

RESULTS

Significant differences among the three groups in bacteria composition and functionality were found by both qPCR and Illumina sequencing analysis. Significant (p < 0.01) differences were found by ANOSIM and Discriminant Analysis among groups at the family, genus and species levels in both microbiota composition and functionality. A number of groups able to explain the differences between animal (casein, lactalbumin) and lupin proteins were revealed by LEfSe and PCA analysis. Specifically, feeding the CAS diet resulted in lower Bifidobacteria and Lactobacilli compared to the other diets, and the LPI diet gave place to lower Enterobacteria than CAS, and lower Escherichia/Shigella than LA and CAS. Differences in the LA group were attributable to Bifidobacterium spp., Collinsella spp. (in particular C. stercoris), Bacteroides spp., Eubacterium spp. (in particular E. dolichum), Roseburia spp. (in particular R. faecis), and Oscillospira spp. In the case of the CAS group, the organisms were Parabacteroides spp., Blautia spp., Enterobacteriaceae spp., Turicibacter spp., species from Christenellaceae, species from Alphaproteobacteria and Mogibacteriaceae, Coprobacillus spp. and Dorea spp. In the case of the LPI group, the organisms were Lactobacillus spp. (Lactobacillus spp. and L. reuteri), species from Clostridiaceae, species from Peptostreptococcaceae, species from Erysipelotrichaceae, and Adlercreutzia spp.

CONCLUSIONS

Based on the results obtained, LPI is likely to beneficially modulate the intestinal microbiota composition in rats. Additionally, LA-based diet was associated to a healthier microbiota composition than CAS, although the CAS diet also modulated the intestinal microbiota to a composition compatible with improved bowel movement frequency and lipid metabolism.

Energetic and genomic potential for hydrogenotrophic, formatotrophic, and acetoclastic methanogenesis in surface-expressed serpentinized fluids of the Samail Ophiolite

Serpentinization, the reaction of water with ultramafic rock, produces reduced, hyperalkaline, and H2-rich fluids that support a variety of hydrogenotrophic microbial metabolisms. Previous work indicates the occurrence of methanogenesis in fluids from the actively serpentinizing Samail Ophiolite in the Sultanate of Oman. While those fluids contain abundant H2 to fuel hydrogenotrophic methanogenesis (CO2 + 4H2 ➔ CH4 + 2H2O), the concentration of CO2 is very low due to the hyperalkalinity (> pH 11) and geochemistry of the fluids. As a result, species such as formate and acetate may be important as alternative methanogenic substrates. In this study we quantified the impact of inorganic carbon, formate and acetate availability for methanogenic metabolisms, across a range of fluid chemistries, in terms of (1) the potential diffusive flux of substrates to the cell, (2) the Affinity (Gibbs energy change) associated with methanogenic metabolism, and (3) the energy "inventory" per kg fluid. In parallel, we assessed the genomic potential for the conduct of those three methanogenic modes across the same set of fluids and consider the results within the quantitative framework of energy availability. We find that formatotrophic methanogenesis affords a higher Affinity (greater energetic yield) than acetoclastic and hydrogenotrophic methanogenesis in pristine serpentinized fluids and, in agreement with previous studies, find genomic evidence for a methanogen of the genus Methanobacterium to carry out formatotrophic and hydrogenotrophic methanogenesis, with the possibility of even using bicarbonate as a supply of CO2. Acetoclastic methanogenesis is also shown to be energetically favorable in these fluids, and we report the first detection of a potential acetoclastic methanogen of the family Methanosarcinaceae, which forms a distinct clade with a genome from the serpentinizing seafloor hydrothermal vent field, Lost City. These results demonstrate the applicability of an energy availability framework for interpreting methanogen ecology in serpentinizing systems.

A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment

The intricate interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host and microbiome across multiple spatial modalities. We demonstrate MicroCart by investigating gut host and microbiome changes in a murine colitis model, using spatial proteomics, transcriptomics, and glycomics. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multi-omics.

Effects of drought stress and Morchella inoculation on the physicochemical properties, enzymatic activities, and bacterial community of Poa pratensis L. rhizosphere soil

Background

Soil microorganisms are crucial for plant growth, and both plants and their associated rhizosphere microbes are impacted by changes in soil moisture. Inoculation with beneficial fungi can improve bacterial community structure and soil parameters.

Aim

Under drought stress conditions, the effects of inoculation with Morchella on the physicochemical properties, enzyme activity, and bacterial community structure of the rhizosphere soil of Poa pratensis were studied.

Methods

High-throughput sequencing was employed to study rhizosphere soil bacterial communities in both Morchella-inoculated and uninoculated Poa pratensis rhizosphere soil subjected to moderate (50% soil moisture) and severe (30% soil moisture) drought stress, as well as under normal water conditions (70% soil moisture).

Results

Morchella inoculation significantly increased the alkaline nitrogen (AN) and available phosphorus (AP) contents, protease activity (PA), and alkaline phosphatase activity (APA) of Poa pratensis rhizosphere soil. Both Morchella inoculation and drought stress significantly altered the abundance and diversity of the P. pratensis rhizosphere community. The Chao1, Shannon, and Pielou diversity indices decreased with increasing drought stress. The effect of Morchella inoculation was improved under moderate drought stress and unstressed conditions. In addition, Morchella inoculation may help to stabilize the rhizosphere bacterial community under various levels of soil moisture.

Effects of yeast culture on growth performance, antioxidant capacity, immune function, and intestinal microbiota structure in Simmental beef cattle

Introduction

As functional feed additives, yeast cultures have been applied in animal husbandry and shown a wide range of good efficacy. This paper aimed to evaluate the effects of yeast culture (YC) on the growth performance, antioxidant capacity, immune function, and intestinal microbiota structure in beef cattle.

Methods

Forty Simmental bulls were randomly divided into two groups, including the control group fed with Total mixed ration (TMR) and YC group fed with TMR supplemented with 2% YC, for 60 days. Serum samples were collected on the 1st, 30th, and 60th days, respectively, while feces 3 days before the end of the test.

Results

Results showed that YC addition significantly elevated average daily gain and reduced feed to weight ratio of beef cattle. The enzyme activities of total superoxide dismutase, total antioxidant capacity, and glutathione peroxidase in the serum in YC group obviously increased, while the malondialdehyde content distinctly decreased. Furthermore, YC feeding significantly enhanced the immunoglobulin G (IgG), IgA, IgM levels, lysozyme content, alkaline phosphatase activity, as well as the contents of interleukin-1β (IL-1β), IL-6, and interferon-γ in the cattle serum. The Shannon and Observed species indexes of fecal samples in YC group were remarkably higher than those in the control group, with the former group exhibiting a significant increase in the relative abundance of Paraprevotellace_CF231 and Peptostreptococcaceae_Clostridium at the genus level, while the relative abundance of Spirochaetaceae_Treponema decreased significantly. Moreover, the abundance of Clostridium and CF231 was positively associated with the levels of serum antioxidant capacity and immune function indicator contents.

Discussion

In conclusion, YC could obviously improve the growth performance, antioxidant capacity, immune function, and intestinal microbiota structure in Simmental beef cattle. These results provide a theoretical basis for the clinical application of such yeast fermented preparations in beef cattle husbandry.

Effects of Limosilactobacillus fermentum KBL375 on Immune Enhancement and Gut Microbiota Composition in Cyclophosphamide-Induced Immunosuppressed Mice

This study evaluated the immune-enhancing efficacy of Limosilactobacillus fermentum KBL375 isolated from the feces of healthy Koreans. KBL375-treated splenocytes showed enhancement of cytotoxicity against YAC-1 cells, the target of natural killer (NK) cells, with an increase in CD335, granzyme B, perforin, and interferon-gamma (IFN-γ). Oral administration of KBL375 in mice with cyclophosphamide (CP)-induced immunosuppression improved body weight and immune functions, including immune organ indices, lymphocyte proliferations, and immunoglobulin (Ig) A levels. Notably, KBL375 increased NK cell cytotoxicity and proportion in immunosuppressed mice. Perforin/IFN-γ expression levels, which indicated NK cell activation, were also increased in KBL375-treated mice. Furthermore, KBL375 led to an increase in beneficial microbes, such as Bifidobacterium, in the gut microbiome of immunosuppressed mice, fostering a favorable intestinal microbial environment. These comprehensive results suggest that KBL375 exhibits potent immune regulatory functions and positively influences the gut microbiota, implying its potential as a probiotic agent for immune enhancement.

A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island

The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.

Probiotics as Renal Guardians: Modulating Gut Microbiota to Combat Diabetes-Induced Kidney Damage

Gut microbiota plays a pivotal role in various health challenges, particularly in mitigating diabetes-induced renal damage. Numerous studies have highlighted that modifying gut microbiota is a promising therapeutic strategy for preserving kidney function and mitigating diabetes-related complications. This study aimed to evaluate the protective effects of Lactobacillus acidophilus ATCC 4356 supplementations on kidney health in a rat model of diabetes-induced renal damage. Four groups were studied: control, probiotic supplementation, diabetic, and diabetic with probiotic supplementation. Diabetes was induced using a single streptozotocin (STZ) injection after a 12 h fast, and probiotic supplementation (1 × 10⁹ CFU/kg daily) was administered two weeks prior to diabetes induction and continued throughout the experimental period. Weekly assessments included fasting blood glucose, insulin, glycation markers, and kidney function tests. Glucose metabolism and insulin sensitivity were analyzed through oral glucose tolerance test (OGTT) and insulin sensitivity test (IST). The microbiome was analyzed using 16S rRNA gene sequencing to evaluate changes in diversity and composition. Probiotic supplementation significantly enhanced microbial diversity and composition. Alpha diversity indices such as Shannon and Chao1 demonstrated higher values in the probiotic-treated diabetic group compared to untreated diabetic rats. The Firmicutes/Bacteroidetes ratio, a key indicator of gut health, was also restored in the probiotic-treated diabetic group. Results: Probiotic supplementation significantly improved glycemic control, reduced fasting blood glucose levels, and enhanced insulin sensitivity in diabetic rats. Antioxidant enzyme levels, depleted in untreated diabetic rats, were restored, reflecting reduced oxidative stress. Histological analysis showed better kidney structure, reduced inflammation, and decreased fibrosis. Furthermore, the Comet assay results confirmed a reduction in DNA damage in probiotic-treated diabetic rats. Conclusion: Lactobacillus acidophilus ATCC 4356 supplementation demonstrated significant protective effects against diabetes-induced renal damage by restoring gut microbiota diversity, improving glycemic control, and reducing oxidative stress. These findings highlight the potential of targeting the gut microbiota and its systemic effects on kidney health as a therapeutic approach for managing diabetes-related complications. Further research is needed to optimize probiotic treatments and assess their long-term benefits in diabetes management and kidney health.

Groundwater denitrification using electro-assisted autotrophic processes: exploring bacterial community dynamics in a single-chamber reactor

Nitrate, a major groundwater pollutant from anthropogenic activities, poses serious health risks when present in drinking water. Denitrification using bio-electrochemical reactors (BER) offers an innovative technology, eco-friendly solution for nitrate removal from groundwater. BER use electroactive bacteria to reduce inorganic compounds like nitrate and bicarbonate by transferring electrons directly from the cathode. In our work, two batch BER were implemented at 1V and 2V, using anaerobic digestate from a full-scale wastewater treatment plant as inoculum. Nitrate, nitrite, sulfate, total ammoniacal nitrogen, and 16S rRNA analysis of bacterial community, were monitored during BER operation. The results showed effective nitrate removal in all BERs, with denitrification rate at 1V and 2V higher than the Control system, where endogenous respiration drove the process. At 1V, complete nitrate conversion to N2 occurred in 4 days, while at 2V, it took 14 days. The slower rate at 2V was likely due to O2 production from water electrolysis, which competed with nitrate as final electron acceptor. Bacterial community analysis confirmed the electroactive bacteria selection like the genus Desulfosporosinus and Leptolinea, confirming electrons transfer without an electroactive biofilm. Besides, Hydrogenophaga was enhanced at 2V likely due to electrolytically produced H2. Sulfate was not reduced, and total ammoniacal nitrogen remained constant indicating no dissimilatory nitrite reduction of ammonia. These results provide a significant contribution to the scaling up of electro-assisted autotrophic denitrification and its application in groundwater remediation, utilizing a simple reactor configuration-a single-chamber, membrane-free design- and a conventional power source instead of a potentiostat.

Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia

Gut microbiota (GM) alterations have been implicated in autism spectrum disorder (ASD), yet the specific functional architecture remains elusive. Here, employing multi-omics approaches, we investigate stool samples from two distinct cohorts comprising 203 children with mild ASD or typical development. In our screening cohort, regression-based analysis for metabolomic profiling identifies an elevated γ-aminobutyric acid (GABA) to glutamate (Glu) ratio as a metabolic signature of ASD, independent of age and gender. In the validating cohort, we affirm the GABA/Glu ratio as an ASD diagnostic indicator after adjusting for geography, age, gender, and specific food-consuming frequency. Integrated analysis of metabolomics, 16S rRNA sequencing, and metagenomics reveals a correlation between overrepresented Escherichia and disrupted GABA metabolism. Furthermore, we observe social behavioral impairments in weaning mice transplanted with E. coli, suggesting a potential link to ASD symptomatology. Collectively, these findings provide insights into potential diagnostic and therapeutic strategies aimed at evaluating and restoring gut microbial neurotransmitter homeostasis.

Reciprocal translocation experiments reveal gut microbiome plasticity and host specificity in a Qinghai-Xizang Plateau lizard

Animal adaptation to environmental challenges is a complex process involving intricate interactions between the host genotype and gut microbiome composition. The gut microbiome, highly responsive to external environmental factors, plays a crucial role in host adaptability and may facilitate local adaptation within species. Concurrently, the genetic background of host populations influences gut microbiome composition, highlighting the bidirectional relationship between host and microbiome. Despite this, our understanding of gut microbiome plasticity and its role in host adaptability remains limited, particularly in reptiles. To clarify this issue, we conducted a reciprocal translocation experiment with gravid females of the Qinghai toad-headed lizards ( Phrynocephalus vlangalii) between high-altitude (2 600 m a.s.l.) and superhigh-altitude (3 600 m a.s.l.) environments on Dangjin Mountain of the Qinghai-Xizang Plateau, China. One year later, we assessed the phenotypes and gut microbiomes of their offspring. Results revealed significant plasticity in gut microbiome diversity and structure in response to contrasting elevations. High-altitude conditions increased diversity, and maternal effects appeared to enable high-altitude lizards to maintain elevated diversity when exposed to superhigh-altitude environments. Additionally, superhigh-altitude lizards displayed distinct gut microbiome structures with notable host specificity, potentially linked to their lower growth rates. Overall, these findings underscore the importance of the gut microbiome in facilitating reptilian adaptation to rapid environmental changes across altitudinal gradients. Furthermore, this study provides critical insights into microbial mechanisms underpinning local adaptation and adaptative plasticity, offering a foundation for future research on host-microbiome interactions in evolutionary and ecological contexts.

Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices

Soil health and One Health are global concerns, necessitating the development of refined indicators for effective monitoring. In response, we present the Anaconda R Package, a novel tool designed to enhance the analysis of eDNA data for biomonitoring purposes. Employing a combination of different approaches, this package allows for a comprehensive investigation of species abundance and community composition under diverse conditions. This study applied the Anaconda package to examine the impact of two types of duration fire-fallow cropping systems, using natural forests as a reference, on soil fungal and bacterial communities in Maré Island (New Caledonia). Condition-specific taxa were identified, particularly pathogenic fungi and bacteria, demonstrating the importance of long-term fallowing efforts. Notably, this package also revealed the potential contributions of beneficial soil microbes, including saprophytes and plant-endophyte fungi, in suppressing soil-borne pathogens. Over-represented microbial ASVs associated with both plant and animal pathogens, including those of potential concern for human health, were identified. This underscores the importance of maintaining intrinsic balance for effective disease suppression. Importantly, the advanced analytical and statistical methods offered by this package should be harnessed to comprehensively investigate the effects of agricultural practice changes on soil health within the One Health framework. Looking ahead, the application of this method extends beyond the realm of One Health, offering valuable insights into various ecological scenarios. Its versatility holds promise for elucidating complex interactions and dynamics within ecosystems. By leveraging this tool, researchers can explore the broader implications of agricultural practice modifications, facilitating informed decisions and sustainable environmental management.

Ecological and Functional Changes in the Hindgut Microbiome of Holstein Cows at High Altitudes

The extreme environmental conditions of the Qinhai-Tibetan Plateau (QTP) challenge livestock survival and productivity, yet little is known about how high-altitude environments impact the gut microbiota of dairy cows. To fill this gap, we systematically investigated the differences in the hindgut microbiome between 87 plateau Holstein cows and 72 plain Holstein cows using 16S rRNA gene sequencing. Our analysis revealed that the hindgut microbiota of the plateau group exhibited lower species richness but higher evenness than that in the plain group. Additionally, significant separation in hindgut microbiota composition between the two groups was observed based on altitude, while parity, days in milk, and age did not show a comparable impact. Moreover, altitude had a lasting impact on bacterial communities and their co-occurrence networks, resulting in reduced microbial interactions and lower modularity in the plateau group. Furthermore, we identified four key microbial taxa, the Bacteroidaceae and Rikenellaceae families, as well as the Prevotella and Treponema genera, which were associated with the regulation of carbohydrate digestion and energy metabolism and might help the Holstein cows adapt to the plateau environment. Our findings provide insights into strategies for enhancing the adaptability of dairy cows to high-altitude environments through microbiota modulation, which could ultimately contribute to improving livestock management and sustainability in these extreme environments.