Multivariable association discovery in population-scale meta-omics studies

Gut microbiota diversity affects fish behaviour and is influenced by host genetics and early rearing conditions

The gut microbiota influences human and animal cognition and behaviour through its effects on the endocrine and immune systems. The microbiome-behaviour relationship may be especially relevant for fish, due to their diverse evolutionary history and potential implications for farming and conservation. Yet, there is limited research on the interaction between gut microbiome and behaviour in non-model fish. We manipulated the rearing environment and diet of fish from two inbred strains of the self-fertilizing mangrove killifish (Kryptolebias marmoratus) and assessed the effects on the gut microbiome and its interactions with anxiety-like behaviours. We found that microbiota composition and alpha diversity were significantly influenced by host genetics (strain), hatching mode (naturally or artificial dechorionation) and diet, but not by environmental enrichment. Fish activity level and inspections of a novel object were strongly associated with microbiota community composition and alpha diversity. The microbial taxa associated with differences in behaviour were dominated by Bacteroidales, potentially related to the production of metabolites affecting neural development. We suggest that the association between microbiome and fish behaviour could be an indirect effect of the modulation of the gut microbiota by host genetics and early rearing conditions, which could be affecting the production of microbial metabolites that interact with the fish physiology.

Phytostabilization potential and microbial response to the reclamation of native Cynodon dactylon in spoil heaps from a multiple-metal mining site in Southwest China

Phytocapping offers a sustainable approach for managing exposed tailings by mitigating pollutant spread and enhancing phytoremediation. This study investigates the potential of Bermudagrass (Cynodon dactylon) as a pioneering plant for rehabilitating tailings from an open-pit lead-zinc mine in Southwest China. Our findings demonstrate that Bermudagrass significantly improved soil quality and multifunctionality compared to adjacent bare tailings. Soil improvements included increases in organic matter (107%), total and available nitrogen (50% and 110%, respectively), available phosphorus (170%), and soil enzyme activities, including β-glucosidase (170%), sucrase (1729%), alkaline phosphatase (3722%), and acid phosphatase (168%). The reclamation process also promoted microbial community succession, altering community composition, improving microbial diversity, and enhancing bacterial biomass from (0.89 ± 0.54) × 1015 to (9.06 ± 3.25) × 1015 copies/g in rhizosphere soils. Greenhouse experiments further confirmed Bermudagrass's resilience to cadmium (Cd), with both mining and non-mining ecotypes thriving in tailing soils and Cd2+ hydroponic solutions (up to 44.5 μM) without evident phytotoxicity. Bermudagrass roots exhibited exceptional Cd accumulation (bioconcentration factor: 181-1006) while minimizing Cd translocation to shoots (translocation factor: <0.13). Inoculation with Funneliformis mosseae, a restored root-mutually symbiotic fungus, further mitigated Cd-induced phytotoxicity and enhanced plant growth. These findings highlight Bermudagrass as a promising pioneer species for phytostabilization in severely contaminated mining environments, with its rhizosphere microbiome playing a critical role in facilitating ecosystem restoration. Sustainable plant establishment in mine waste rock requires concurrent development of belowground fertility and healthy rhizospheric soil. Ultimately, successful revegetation depends on integrated above and belowground development to achieve long-term ecological restoration.

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types

The relationship between the oral microbiome and oral squamous cell carcinoma (OSCC) has been extensively investigated. Nonetheless, most previous studies were single-center, resulting in the absence of systematic evaluations. To address this gap, we performed a comprehensive meta-analysis on 1,255 samples from OSCC-related 16S rRNA gene data sets, representing a diverse range of OSCC phenotypes. It is recognized that the progression of cancer is related to the alterations in the microbiome among different phenotypes. Our findings revealed distinct microbiome characteristics among different sample types, with Biopsy (Bios) and Swab samples exhibiting significant differences between phenotypes. In Bios samples, the microbiomes of the Cancer group and the normal tissue adjacent to the tumor (NAT) group display a higher similarity, while both differ from the microbiome of the Fibroepithelial polyp (FEP) group. Moreover, the identified differential genera and pathways corresponded with these observations. We developed a diagnostic model using the random forest algorithm on Swab samples, achieving an area under the receiver operating characteristic curve (AUC) of 0.918. Importantly, this model exhibited considerable effectiveness (AUC = 0.849) when applied to another sequencing platform. Taken together, our study provides a comprehensive overview of the oral microbiome during various OSCC progression stages, potentially enhancing early detection and treatment.IMPORTANCEThis study answers key questions regarding the universal microbial characteristics and comprehensive oral microbiome dynamics during oral squamous cell carcinoma (OSCC) progression. By integrating multiple data sets, we examine the following critical aspects: (1) Do different sample types harbor distinct microbial communities within the oral cavity? (2) Which sample types offer greater potential for investigating OSCC progression? (3) How are the oral microbiomes of the Cancer group, normal tissue adjacent to the tumor group, and Fibroepithelial polyp group related, and what is their potential association with OSCC development? (4) Can a diagnostic model based on microbial signatures effectively distinguish between Cancer and Health groups using Swab samples?

Best Practices and Considerations for Conducting Research on Diet-Gut Microbiome Interactions and Their Impact on Health in Adult Populations: An Umbrella Review

Diet modulates gut microbiome composition and function. However, determining causal links between diet-gut microbiome interactions and human health is complicated by inconsistencies in the evidence, arising partially from variability in research methods and reporting. Widespread adoption of standardized best practices would advance the field but require those practices to be identified, consolidated, and discussed. This umbrella review aimed to identify recommended best practices, define existing gaps, and collate considerations for conducting research on diet-gut microbiome interactions and their impact on human health outcomes. Reviews meeting inclusion criteria and published after 2013 were identified using a systematic search. Recommendations, considerations, and gaps relating to the best practices associated with study design, participant selection, dietary intervention/assessment, biological sample collection, and data analysis and reporting were extracted and consolidated. Eight narrative reviews were included. Several general points of agreement were identified, and a recurring theme was that best practices are dependent upon the research aims, outcomes, and feasibility. Multiple gaps were also identified. Some, such as suboptimal diet assessment methods and lack of validated dietary intake biomarkers, are particularly relevant to nutrition science. Others, including defining a "healthy" gut microbiome and the absence of standardized sample and data collection/analysis protocols, were relevant specifically to gut microbiome research. Gaps specific to diet-gut microbiome research include the underrepresentation of microbiome-modulating dietary components in food databases, lack of knowledge regarding interventions eliciting changes in the gut microbiome to confer health benefits, lack of in situ measurement methods, and the need to further develop and refine statistical approaches for integrating diet and gut microbiome data. Future research and cross-disciplinary exchange will address these gaps and evolve the best practices. In the interim, the best practices and considerations discussed herein, and the publications from which that information was extracted provide a roadmap for conducting diet-gut microbiome research. This trial was registered at PROSPERO as CRD42023437645.

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice

The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.

Comparison of microbiome community structure and dynamics during anaerobic digestion of different renewable solid wastes

This study analysed the effect of the different lignocellulose composition of two crop substrates on the structure and dynamics of bacterial communities during anaerobic digestion (AD) processes for biogas production. To this end, cereal grains and grape pomace biomasses were analysed in parallel in an experimental AD bench-scale system to define and compare their metagenomic profiles for different experimental time intervals. The bacterial community structure and dynamics during the AD process were detected and characterised using high-resolution whole metagenomic shotgun analyses. Statistical evaluation identified 15 strains as specific to two substrates. Some strains, like Clostridium isatidis, Methanothermobacter wolfeii, and Methanobacter sp. MB1 in cereal grains, and Acetomicrobium hydrogeniformans and Acetomicrobium thermoterrenum in grape pomace, were never before detected in biogas reactors. The presence of bacteria such as Acetomicrobium sp. and Petrimonas mucosa, which degrade lipids and protein-rich substrates, along with Methanosarcina sp. and Peptococcaceae bacterium 1109, which tolerate high hydrogen pressures and ammonia concentrations, suggests a complex syntrophic community in lignin-cellulose-enriched substrates. This finding could help develop new strategies for the production of a tailor-made microbial consortium to be inoculated from the beginning of the digestion process of specific lignocellulosic biomass.

Comparative analysis of oral microbiome in molar-incisor-hypomineralization vs healthy age-matched controls

Molar-incisor-hypomineralization (MIH) is one of the most challenging dental diseases in children. While the association of oral microbiomes with caries and periodontitis has been studied thoroughly, limited data on the microbial composition in MIH and its clinical significance exist. This cross-sectional study aimed to compare the supragingival plaque microbiome between children and adolescents affected by MIH and a healthy age-matched control group. Ninety-five patients aged 7-17 years were recruited at the Department of Conservative Dentistry, Heidelberg University Hospital. The final sample included 29 participants with a confirmed diagnosis of MIH, treated preventively and restoratively, and 35 orally healthy controls. Clinical data were obtained, and supragingival plaque samples were collected using OMNIgene ORAL OMR-110 (DNA Genotek Inc.), followed by 16S rRNA amplicon sequencing. The microbiome composition was analyzed using α-diversity (Shannon index) and evenness (Pielou index), with group differences assessed using permutational multivariate analysis of variance (PERMANOVA) and MaAsLin2. The overall microbiome composition showed mostly similarities between both groups (PERMANOVA: R² = 0.019, P-value = 0.287), indicating no major dysbiosis. However, a significant decrease in α-diversity and evenness was observed with an increasing number of MIH-affected teeth. Pronounced positive correlations were found between ASV0055 (Streptococcus spp.), caries experience, and MIH severity. ASV0100 (Mannheimia sp.) increased significantly with the increasing number of MIH-affected teeth, whereas ASV0053 (Bergeyella sp.) decreased with higher caries experience. In summary, the oral microbiome of children and adolescents with MIH exhibits no significant differences from healthy children and adolescents of the same age group. Depending on MIH severity, the presence of early plaque-forming species and cariogenic biofilm may increase, requiring intensive, tailored preventive care and appropriate restorative treatment to achieve microbial homeostasis.

IMPORTANCE

Molar-incisor-hypomineralization (MIH) represents a significant burden for affected children and adolescents, playing an increasingly important role in pediatric dentistry worldwide. Despite its high global prevalence, data on the microbiome of MIH patients remains limited. This study is the first to compare the oral microbiome composition of MIH patients with a healthy control group, making a significant contribution to pediatric dentistry and microbiology. Our results indicate that the oral microbiome of children with MIH is similar to that of healthy children of the same age. Although this structural anomaly predisposes patients to caries, effective preventive and restorative treatments can help maintain microbial homeostasis. However, MIH-affected children remain high-risk patients, as the disease severity may reduce microbial diversity. Furthermore, the increased abundance of Streptococcus spp. in MIH patients indicates a higher caries susceptibility, emphasizing the need for targeted dental care focusing on plaque control and topical fluoride use.

Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.

hTAS2R38 polymorphisms modulate oral microbiota and influence the prevalence and treatment outcome of halitosis

BACKGROUND

The genetic susceptibility of halitosis is unclear, challenging its precise management in high-risk population. Here we investigated the association of hTAS2R38 polymorphisms with the prevalence and treatment outcome of halitosis, with a particular focus on oral microbiota.

METHODS

A cross-sectional study including 689 participants was conducted to investigate the association between hTAS2R38 polymorphisms and halitosis. A 6-month cohort including 60 halitosis patients was established to explore the relationship between hTAS2R38 polymorphisms and treatment outcome of halitosis. Salivary microbiota was further analyzed and its correlation with hTAS2R38 polymorphisms was investigated.

RESULTS

In the cross-sectional study, a higher prevalence of halitosis was observed in individuals with AVI/AVI genotype as compared to non-AVI/AVI genotype (PAV/PAV + PAV/AVI) (OR = 2.380, 95% CI = 1.493-3.807). 16S rRNA sequencing revealed the enrichment of Prevotella in the saliva of AVI/AVI individuals. In the prospective study, halitosis patients with AVI/AVI genotype exhibited poor treatment outcome relative to non-AVI/AVI individuals during the 6-month follow-up after halitosis intervention (RR = 2.077, 95% CI = 1.382-3.339). Tannerella, Filifactor, and Mycoplasma were identified to be the major persistent genus in the saliva of AVI/AVI patients over the 6-month period after treatment. Furthermore, the human gingival fibroblasts with AVI/AVI genotype exhibited reduced inhibition against the growth and volatile sulfur compounds production of periodontal pathogens.

CONCLUSIONS

Our work demonstrates that hTAS2R38 polymorphisms contribute to the development and treatment outcome of halitosis via modulating oral microbiota, providing new insights to the better management of halitosis. Video Abstract.

Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides

The human microbiome produces diverse metabolites that influence host health, yet the chemical landscape of ribosomally synthesized and post-translationally modified peptides (RiPPs)-a versatile class of bioactive compounds-remains underexplored. Here, we conduct a large-scale biosynthetic analysis of 306,481 microbial genomes from human-associated microbiomes, uncovering a broad array of yet-to-be-discovered RiPPs. These RiPPs are distributed across various body sites but show a specific enrichment in the gut and oral microbiome. Big data omics analysis reveals that numerous RiPP families are inversely related to various diseases, suggesting their potential protective effects on health. For a proof of principle study, we apply the synthetic-bioinformatic natural product (syn-BNP) approach to RiPPs and chemically synthesize nine autoinducing peptides (AIPs) for in vitro and ex vivo assay. Our findings reveal that five AIPs effectively inhibit the biofilm formation of disease-associated pathogens. Furthermore, when ex vivo testing gut microbiota from mice with inflammatory bowel disease, we observe that two AIPs can regulate the microbial community and reduce harmful species. These findings highlight the vast potential of human microbial RiPPs in regulating microbial communities and maintaining human health, emphasizing their potential for therapeutic development.

Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology

BACKGROUND

Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.

RESULTS

We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics of this primarily aerial disease.

CONCLUSION

Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.

Inhibitory control is related to fecal short-chain fatty acid concentrations in adults with overweight and obesity

Obesity is a pro-inflammatory condition with negative effects on executive functioning. Increased inflammation dysregulates gastrointestinal homeostasis and alters microbiota community composition. The gut microbiota produce immunomodulatory short-chain fatty acids (SCFA) that have been related to cognition in obesity, but the neural effects are not explored. Here, we hypothesized that greater fecal SCFA would be positively related to neuroelectric markers of inhibitory control and conflict monitoring in obesity. A cross-sectional cohort of 87 adults (35 ± 6 years, 53 females) with overweight and obesity (BMI = 32 ± 6 kg/m2) provided fresh fecal samples and participated in cognitive testing to assess response inhibition and conflict monitoring with electroencephalographic recording. Linear regressions, controlling for age, sex, BMI, and energy-adjusted dietary fiber intake, revealed positive relationships between NoGo N2 mean amplitude and fecal SCFA concentrations. Linear discriminant analysis effect size (LEfSe) revealed 16 amplicon sequence variants differentially abundant between high and low butyrate groups with Roseburia and Adlercreutzia individually related to NoGo N2 mean amplitude in MaAsLin2 modeling. Thus, greater fecal SCFA concentrations and SCFA producing microbiota (i.e., Roseburia) were related to markers of superior conflict monitoring in the NoGo task when adjusting for key covariates. These data highlight key associations between bacterial derived gut signaling molecules and neural regulation in cognitive domains particularly relevant to weight status that warrant further investigation.

Virus-induced perturbations in the mouse microbiome are impacted by microbial experience

The bacterial microbiome has a major impact on health and can shape metabolism, host tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen-free animals have reduced microbiome diversity, making it difficult to evaluate the impact of infection-induced microbiome disruption that would be observed in free-living animals, including people. Mice are commonly used as a preclinical model but unfortunately often fail to predict translation success or failure, particularly for immune and infectious disease-targeting therapies. Here, we utilize pet store mouse cohoused "dirty" mice with diverse microbial experience to explore how host variability and infection may be interacting to drive unique microbiome changes. We found that cohoused animals had significantly increased bacterial diversity in the small intestine and cecum but not in the large intestine. There were differentially abundant taxa between clean and dirty animals in all three tissues. After infection with influenza A virus, samples clustered by both housing condition and infection status in the cecum and large intestine, while small intestine samples clustered predominantly by infection. Altogether, these results highlight the differential impact of housing, infection, and interaction between the two in dictating community composition across the gastrointestinal microbiome.IMPORTANCETraditionally housed pathogen-free mouse models do not fully capture the natural variability observed among human microbiomes, which may underlie their poor translationally predictive value. Understanding the difference between pathogen-induced shifts in the bacterial microbiome and natural microbiome variance is a major hurdle to determining bacterial biomarkers of disease. It is also critical to understand how diverse baseline microbiomes may be differentially impacted by infection and contribute to disease. Pet store cohoused "dirty" mice have diverse microbial experiences and microbiomes, allowing us to evaluate how baseline variation, infection, and interaction between the two impact the microbiome.

Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome

BACKGROUND

Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.

RESULTS

We studied a cohort of febrile term infants < 60 days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (> 99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.

CONCLUSIONS

The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.

Impact of dietary polyphenols from shredded, steam-exploded pine on growth performance, organ indices, meat quality, and cecal microbiota of broiler chickens

The chicken's gastrointestinal tract is home to complex and diverse microbial communities that can be manipulated to enhance health and productivity. Although polyphenols have recently attracted the attention of researchers due to their potent antioxidant capabilities, their impact on the gut microbiota remains largely unexplored. Hence, in this study, we conducted a comprehensive analysis of the effects of dietary supplementation with polyphenol-rich extract from shredded, steam-exploded pine particles (PSPP) on growth, meat quality, and gut microbial dynamics in broiler chickens. Supplementation of PSPP was found to significantly improve birds' FCR until the third week of the trial but only marginally affected meat quality. Based on metataxonomic analyses of the cecal microbiotas of broilers fed increasing concentrations of PSPP, dietary PSPP modulated the composition of the cecal microbiota of the birds with a concomitant increase of Bacteroidetes and a decrease in the Firmicutes population. Similar trends were observed for the proportions of Alistipes and Faecalibacterium at the genus level. Additionally, 43 unique bacterial species were detected in the cecal microbiome of birds fed with PSPP. However, microbial diversity did not vary significantly among treatment groups. A particularly interesting finding was the specialization observed in the microbiome of birds receiving PSPP supplementation. Microbial co-occurrence network analyses revealed substantial modifications in their network structure when compared to control birds. Families like Rikenellaceae and Eubacteriaceae were notably absent, and the number of microbial interactions was drastically lower in the PSPP-fed group. Microbial taxa modeling revealed that the impact of increasing dietary PSPP levels primarily affected genus-level taxa, showing a decreasing trend. Overall, this offers compelling evidence that continuous PSPP supplementation may not only alter the composition of intestinal microbes but also have a profound effect on the interactions among different microbial species. Conversely, PSPP had minimal effects on broilers' performance and meat quality.

Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors

BACKGROUND

Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.

METHODS

Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.

RESULTS

Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3+ CD4+ T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14+ and CD16+ monocyte populations were decreased in these individuals.

CONCLUSION

These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.

Metatranscriptomic analysis reveals gut microbiome bacterial genes in pyruvate and amino acid metabolism associated with hyperuricemia and gout in humans

Several pathologies with metabolic origin, such as hyperuricemia and gout, have been associated with the gut microbiota taxonomic profile. However, there is no evidence of which bacterial genes are being expressed in the gut microbiome, and of their potential effects on hyperuricemia and gout. We sequenced the RNA of 26 fecal samples from 10 healthy normouricemic controls, 10 with asymptomatic hyperuricemia (AH), and six gout patients. The coding sequences were mapped to KEGG orthologues (KO). We compared the expression levels using generalized linear models and validated the expression of four KO in a larger sample by qRT-PCR. A distinct genetic expression pattern was identified among groups. AH individuals and gout patients showed an over-expression of KOs mainly related to pyruvate metabolism (Log2foldchange > 23, p-adj ≤ 3.56 × 10- 9), the pentose pathway (Log2foldchange > 24, p-adj < 1.10 × 10-12) and purine metabolism (Log2foldchange > 22, p-adj < 1.25 × 10- 7). AH subjects had lower expression of KO related to glycine metabolism (Log2foldchange=-18, p-adj < 1.72 × 10-6) than controls. Gout patients had lower expression (Log2foldchange=-22.42, p-adj < 3.31 × 10- 16) of a KO involved in phenylalanine biosynthesis, in comparison to controls and AH subjects. The over-expression seen for the KO related to pyruvate metabolism and the pentose pathway in gout patients´ microbiome was validated. There is a differential gene expression pattern in the gut microbiome of normouricemic individuals, AH subjects and gout patients. These differences are mainly located in metabolic pathways involved in acetate precursors and bioavailability of amino acids.

Medication-resistant epilepsy is associated with a unique gut microbiota signature

OBJECTIVE

Dysfunction of the microbiota-gut-brain axis is emerging as a new pathogenic mechanism in epilepsy, potentially impacting on medication response and disease outcome. We investigated the composition of the gut microbiota in a cohort of medication-resistant (MR) and medication-sensitive (MS) pediatric patients with epilepsy.

METHODS

Children with epilepsy of genetic and presumed genetic etiologies were evaluated clinically and subgrouped into MR and MS. Age-matched healthy controls (HCs) were also recruited. A food diary was used to evaluate nutritional habits, and the Rome IV questionnaire was used to record gastrointestinal symptoms. The microbiota composition was assessed in stool samples through 16S rRNA. α-Diversity (AD) and β-diversity (BD) were calculated, and differential abundance analysis was performed using linear multivariable models (significance: p.adj < .05).

RESULTS

Forty-one patients (MR:MS = 20:21) with a mean age of 7.2 years (±4.6 SD) and 27 age-matched HCs were recruited. No significant differences in AD were found when comparing patients and HCs. Significant positive correlation was found between AD and age (Chao1 p.adj = .0004, Shannon p.adj = .0004, Simpson p.adj = .0028). BD depicted a different bacterial profile in the epilepsy groups compared to HCs (MS vs. HC: Bray-Curtis F = 1.783, p = .001; Jaccard F = 1.24, p = .001; MR vs. HC: Bray-Curtis F = 2.24, p = .001; Jaccard F = 1.364, p = .001). At the genus level, the epilepsy groups were characterized by a significant increase in Hungatella (MS vs. HC: +4.95 log2 change; MR vs. HC: +6.72 log2 change); the [Eubacterium] siraeum group changed between the MR and MS subgroups.

SIGNIFICANCE

Epileptic patients display unique gut metagenomic signatures compared to HCs. Moreover, a different ratio of the butyrate-producing [Eubacterium] siraeum group suggests dissimilarities between patients based on the response to antiseizure medications.

Berry supplementation in healthy volunteers modulates gut microbiota, increases fecal polyphenol metabolites and reduces viability of colon cancer cells exposed to fecal water- a randomized controlled trial

Diets high in red and processed meat and low in plant-based foods are associated with an increased risk of colorectal cancer. We investigated whether berry supplementation can impact gut metabolism to counteract the presumably cancer promoting luminal environment sustained by high red and processed meat consumption. Altogether 43 healthy adults were randomized either into Meat group (150 g/d red and processed pork meat) or Meat & Berries group (150 g/d red and processed meat and 200 g/d of mixed berries). Fecal samples and 3-d food records were collected at baseline and at the end of the four-week intervention. Intakes of vitamin C, vitamin E, manganese, insoluble fiber, and the polyphenols available in the database were significantly higher in the Meat & Berries than Meat group. While between-group comparisons found no significant differences in the gut microbiota, the within-group analyses showed that the relative abundances of beneficial Roseburia and Faecalibacterium were decreased and an unclassified group of Peptostreptococcaceae increased significantly in the Meat group. In comparison to the Meat group, berry consumption resulted in higher fecal concentrations of p-coumaric and protocatechuic acids and lower viability of fecal water (FW) -treated CV1-P fibroblastoma and human colon adenocarcinoma HCA-7 and Caco-2 cells (P<.05 with 30% FW). Berry consumption provided protective nutrients and mitigated potentially unfavourable gut microbiota changes seen in the Meat group, increased fecal polyphenol metabolites, and reduced viability of FW-treated colon adenocarcinoma cells, collectively suggesting that berries may protect against colorectal cancer development.

Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis

BACKGROUND

The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.

METHODS

Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.

RESULTS

Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy > 90% and AUC ROC > 95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.

CONCLUSION

The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.

Early-life gut microbiome is associated with behavioral disorders in the Rio birth cohort

Emerging evidence has been linking changes in the early-life gut microbiome and neurodevelopmental outcomes. The founder bacteria that first colonize the infant's gut determine the microbial succession that signals host tissues and impact development including the brain. Here we investigated the association between the meconium microbiome and neurobehavior. To this end, we surveyed the 16S rRNA gene on meconium samples and assessed behavioral outcomes at six-months of age by the Denver Developmental Screening Test II (DDST-II). Among the four behavioral domains investigated, the personal-social domain was associated with significant differences in meconium bacterial beta diversity (unweighted UniFrac; R2 0.078, p = 0.021) and reduced alpha diversity (β = -2.290, 95% CI = -4.212; CI = -0.368), after adjustment for gestational antibiotics, preterm delivery, and delivery mode. Besides, this altered neurobehavior (failing to meet the milestone) was associated with overrepresented Ruminococcaceae, Christensenellaceae, and Eubacterium, Treponema, Senegalimassilia, Ruminiclostridium, Roseburia, Romboutsia, Prevotella, and Veillonella seminalis. Predicted functional genes showed reduced abundance in association with altered neurobehavior (all q < 0.15). Fine and gross motor skills presented no associations with the microbiome. This pilot study shows associations between the first gut microbiome and behavioral outcomes that deserve further studies in different neonate populations.

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis

The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.

Fecal Microbiome and Urine Metabolome Profiling of Type 2 Diabetes

Type 2 diabetes is a prevalent metabolic disorder with serious health consequences, necessitating both enhanced diagnostic methodologies and comprehensive elucidation of its pathophysiological mechanisms. We compared fecal microbiome and urine metabolome profiles in type 2 diabetes patients versus healthy controls to evaluate their respective diagnostic potential. Using a cohort of 94 subjects (48 diabetics, 46 controls), this study employed 16S rRNA amplicon sequencing for fecal microbiome analysis and GC-MS for urinary metabolomics. While fecal microbiome alpha diversity showed no significant differences between groups, urinary metabolomics demonstrated distinct structural patterns and higher evenness in type 2 diabetes patients. The study identified several diabetes-associated urinary metabolites, including elevated levels of glucose and inositol, along with decreased levels of 6 urine metabolites including glycolic acid, hippurate, and 2-aminoethanol. In the fecal microbiome, genera such as Escherichia-Shigella showed positive correlation with type 2 diabetes, while Lacticaseibacillus demonstrated negative correlation. Receiver operating characteristic curve analyses revealed that urinary metabolites exhibited superior diagnostic potential compared to fecal microbiome features, with an area under the curve of 0.90 for the combined metabolite model versus 0.82 for the integrated bacterial taxa model. These findings suggest that urinary metabolomics may offer a more reliable approach for type 2 diabetes diagnosis compared to fecal 16S metabarcoding, while highlighting the potential of multi-marker panels for enhanced diagnostic accuracy.

Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial

Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable cardiometabolic benefits were observed independently of L. reuteri administration, several of which could be accurately predicted by baseline and diet-responsive microbiome features. The findings suggest that a dietary intervention targeted toward restoring the gut microbiome can improve host-microbiome interactions that likely underpin chronic pathologies, which can guide dietary recommendations and the development of therapeutic and nutritional strategies.

Investigating the gut microbiome in schizophrenia cases versus controls: South Africa's version

Schizophrenia (SCZ) is a chronic and severe mental disorder with a complex molecular aetiology. Emerging evidence indicates a potential association between the gut microbiome and the development of SCZ. Considering the under-representation of African populations in SCZ research, this study aimed to explore the association between the gut microbiome and SCZ within a South African cohort. Gut microbial DNA was obtained from 89 participants (n = 41 SCZ cases; n = 48 controls) and underwent 16S rRNA (V4) sequencing. Data preparation and taxa classification were performed with the DADA2 pipeline in R studio followed by diversity analysis using QIIME2. Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) was utilised to identify differentially abundant taxa. No statistically significant differences were observed between SCZ patients and controls in terms of alpha-diversity (Shannon q = 0.09; Simpson q = 0.174) or beta-diversity (p = 0.547). Five taxa, namely Prevotella (p = 0.037), Faecalibacterium (p = 0.032), Phascolarctobacterium (p = 0.002), Dialister (p = 0.043), and SMB53 (p = 0.012), were differentially abundant in cases compared to controls, but this observation did not survive correction for multiple testing. This exploratory study suggests a potential association between the relative abundance of Prevotella, Faecalibacterium, Phascolarctobacterium, Dialister, and SMB53 with SCZ case-control status. Given the lack of significance after correcting for multiple testing, these results should be interpreted with caution. Mechanistic studies in larger samples are warranted to confirm these findings and better understand the association between the gut microbiome and SCZ.

Elementary methods provide more replicable results in microbial differential abundance analysis

Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.

Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility

The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.

Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission

This study aimed to analyze the gut phageome in Japanese patients with ulcerative colitis (UC) in endoscopic remission. Fecal samples were collected from 35 UC patients and 22 healthy controls. The gut microbiome was analyzed using 16S rRNA amplicon sequencing, and the phageome was profiled through shotgun metagenomic sequencing. Compared to healthy controls, UC patients showed a significant reduction in phageome richness (observed species and Chao1 index). Principal coordinate analysis revealed a significant difference in beta-diversity between UC and healthy controls (p = 0.001). The abundance of temperate phages was higher in UC (15.2%) compared to healthy controls (5.9%), although this was not statistically significant (p = 0.088). Temperate phages associated with Coprococcus sp., Bacteroides sp. KFT8, and Faecalibacterium prausnitzii, as well as virulent phages associated with Ruminococcus gnavus and Lactobacillus farciminis, were increased in UC patients. Conversely, phages associated with Thermosipho affectus, Bacteroides sp. OF03-11BH, and Odoribacter splanchnicus were decreased in UC patients. Phages associated with the genera Odoribacter (p = 0.0004), Ruminococcus (p = 0.009), and Veillonella (p = 0.013) were significantly reduced in UC patients. The gut phageome of inactive UC patients exhibited notable alterations in viral composition compared to healthy controls. These results suggest that changes in the gut phageome might be involved in the pathogenesis of UC.

Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease

OBJECT

Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.

METHOD

A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.

RESULT

Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.

CONCLUSIONS

Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.

Life on the edge: mineral incrustations colonized by fungal communities in the sulfur fumarole on Sierra Negra volcano (Galápagos Archipelago)

Despite the extensive studies on plant and animal endemism in the Galápagos Islands, fungal diversity remains largely unexplored, particularly in fumarole environments. Here, we explore the fungal diversity in two gypsum incrustations within an active fumarole of Sierra Negra volcano (Isabela Island). We hypothesize that minor differences in the chemical and mineralogical characteristics of these substrates, despite similar environmental conditions, lead to distinct fungal communities with substrate-specialized taxa. Alpha diversity indices showed no significant differences, but beta diversity analysis revealed two distinct fungal communities (PERMANOVA p < 0.01), with only 3.31% of operational taxonomic units (OTUs) shared between incrustations and 37.75 and 14.57% uniquely associated with each incrustation. A strong correlation was found between beta diversity and most measured chemical parameters (Mg, S, Fe, Na, Al, Mn, Zn, K, P, Cu). Our findings indicate that even minor differences in the mineral and chemical composition of closely located incrustations significantly influence fungal communities, emphasizing these deterministic factors as key drivers in shaping fungal diversity.

Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals

Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.

Overcrowding Stress in Livestock Production Alters Gut Microbiota Composition and Neuronal Nitric Oxide Synthase (nNOS) Expression in nNOS-HiBiT Knock-in Mouse Model

Overcrowding stress in livestock farming is a significant concern for animal health and livestock products such as meats, milk, and eggs. It affects gut health by altering microbiota and regulating neuronal nitric oxide synthase (nNOS). This study aimed to investigate the effects of overcrowding stress on the gut microbiota composition and nNOS expression. We generated an nNOS-HiBiT knock-in mouse model using the HiBiT system, a highly sensitive tool for accurately quantifying gene expression. Overcrowding stress was induced by housing twenty mice per cage (MPC20) and compared with a control group of two mice per cage (MPC2). Overcrowding stress increases nNOS levels in the hypothalamus and ileum and serum corticosterone levels. Gut microbial composition differed between the control and overcrowding stress-induced groups in the ileum, cecum, and colon. Specifically, Bifidobacterium and Akkermansia decreased in all three regions of MPC20, whereas Helicobacter in the ileum and colon and Parasuterella in the cecum increased in MPC20. Notably, Bifidobacterium consistently decreased when nNOS and corticosterone expression were used as covariates under overcrowding stress. These regional variations reflect the differential impact of overcrowding stress on the intestinal tract, indicating complex interactions through nNOS expression within the brain-gut-microbiome axis. Importantly, the addition of probiotic feed, particularly those containing Bifidobacterium, may counteract these decreases, leading to enhanced gut health and improved quality of livestock food products. This study enhances our understanding of the correlation between overcrowding stress and the gut microbiota, providing valuable data for improving the management environment in livestock farming.

Environmental enrichment-induced cognitive recovery after a moderate pediatric traumatic brain injury is associated with the gut microbiota and neuroinflammation

Pediatric traumatic brain injury (TBI) is a significant health concern, yet access to rehabilitation therapies for children remains limited. Environmental enrichment (EE) is a preclinical model of neurorehabilitation that promotes behavioral recovery and reduces neuroinflammation after TBI. While the gut microbiota has recently emerged as a potential therapeutic target for treating TBI sequelae in adults, its role in recovery after pediatric TBI remains unclear. Therefore, our aim was to assess the effect of EE on gut microbiota and its correlation with cognition as well as microglial morphology in a preclinical model of pediatric TBI. Male rats underwent a controlled cortical impact of moderate severity or sham injury at postnatal day 21 and were then randomly assigned to either EE or standard (STD) housing. Cognition was evaluated using the Morris water maze (MWM) on post-injury days 14-19. Microglial morphology and caecum microbiota was characterized on post-injury day 21. Cognitive deficits and increased microglial activation in the ipsilateral cortex were observed in the STD-housed TBI rats but not those in EE. TBI decreased microbiota α-diversity, while PERMANOVA analysis showed that both TBI and EE modified microbiota β-diversity. Furthermore, regression models indicated that microglial morphology in the ipsilateral cortex and Lactobacillus reuteri predicted behavioral outcomes, while Prevotellaceae NK3B31 was associated with microglial morphology. The data suggest that EE mitigates TBI-induced alterations in gut microbiota and that there is a complex interplay between EE, microbiota and microglial morphology that predicts behavioral recovery in pediatric rats.

Mode of Action of Psyllium in Reducing Gas Production from Inulin and its Interaction with Colonic Microbiota: A 24-hour, Randomized, Placebo-Controlled Trial in Healthy Human Volunteers

BACKGROUND

Recent studies show that the increase in breath hydrogen (BH2) and symptoms after ingestion of inulin are reduced by coadministering psyllium (PI).

OBJECTIVES

To determine if slowing delivery of inulin to the colon by administering it in divided doses would mimic the effect of PI. Primary endpoint was the BH2 area under the curve AUC0-24 h. Secondary endpoints included BH2 AUC0-6 h, 6-12 h, and 12-24 h. Exploratory endpoints included the correlation of BH2 AUC0-24 h with dietary fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) intake and in vitro fermentation results.

METHODS

A total of 17 healthy adults were randomly assigned to a single-blind, 3-arm, crossover trial. All consumed 20 g inulin (I) powder dissolved in 500 mL water and mixed with either 20 g maltodextrin (control) or 20 g PI consumed as a single dose or 20 g inulin given in divided doses (DDI), 62.5 mL every 45 min over 6 h. Twenty-four-hour BH2, dietary FODMAP intake, stool microbiota, and gas production in vitro were measured. Responders were defined as those whose AUC0-24 h BH2 was reduced by PI, whereas nonresponders showed no reduction.

RESULTS

Compared with control, PI did not reduce mean BH2 AUC0-24 h, whereas DDI increased it, P < 0.0002. DDI and PI both significantly reduced BH2 AUC0-6 h compared with the control, P < 0.0001. However, subsequently, DDI significantly increased BH2 from 6 to 12 h (P < 0.0001) and overnight (12-24 h) (P < 0.0001), whereas PI did so only overnight (P = 0.0002). Nonresponders showed greater release of arabinose during in vitro fermentation and higher abundance of 2 species, Clostridium spp. AM22_11AC and Phocaeicola dorei, which also correlated with BH2 production on PI. Dietary FODMAP intake tended to correlate inversely with BH2 AUC0-24 h (r = -0.42, P = 0.09) and correlated with microbiome community composition.

CONCLUSIONS

DDI, like PI, reduces early BH2 production. PI acts by delaying transit to the colon but not reducing colonic fermentation over 24 h. Dietary FODMAP intake correlates with BH2 response to inulin and the microbiome. This trial was registered at www.

CLINICALTRIALS

gov as NCT05619341.

Impact of Antibiotic Duration on Gut Microbiome Composition and Antimicrobial Resistance: A Substudy of the BALANCE Randomized Controlled Trial

Background

Maintaining a diverse gut microbiome and minimizing antimicrobial resistance gene (ARG) carriage through reduced antibiotic utilization may decrease antimicrobial resistance. We compared gut microbiome disruption and ARG carriage following 7 or 14 days of antibiotics for treatment of bacteremia in a substudy of the BALANCE randomized controlled trial.

Methods

The BALANCE randomized controlled trial enrolled 3631 participants with bacteremia, who were randomized 1:1 to receive 7 or 14 days of antibiotics. Rectal swabs were collected from 131 participants and analyzed with metagenomic sequencing to characterize the gut microbiome and ARGs. The primary outcome was change in gut microbiome diversity at day 7 vs 14.

Results

Forty-one participants (n = 28 in the 14-day group, n = 13 in the 7-day group) had samples available for the primary analysis, with an imbalance in piperacillin-tazobactam exposure between groups. Change in gut microbiome diversity at day 7 vs 14 was comparable between the 14-day group (median, 0.07; IQR, -0.46 to +0.51) and 7-day group (median, 0.19; IQR, -0.77 to +0.22; P = .49). Change in ARG abundance at day 7 vs 14 did not differ by treatment duration, nor did the abundance of individual ARGs. We did not observe any change in gut microbiome diversity or ARG carriage at enrollment vs day 7.

Conclusions

In this subset of patients from the BALANCE randomized controlled trial, we did not detect greater gut microbiome disruption or ARG carriage among participants who received 14 vs 7 days of antibiotics, but we were limited by small sample size and imbalances between groups.

The association of gut microbiome composition with musculoskeletal features in middle-aged and older adults: a two-cohort joint study

Background

Bones and muscles are connected anatomically, and functionally. Preliminary evidence has shown the gut microbiome influences the aging process of bone and muscle in animal studies. However, such evidence in humans is still scarce. This study aimed to assess the microbiome-bone and microbiome-muscle associations in two cohorts of community-dwelling older adults.

Methods

We leveraged information from two large population-based cohorts, i.e., the Rotterdam Study (mean age 62.7 ± 5.6 years; n=1,249) and the Framingham Heart Study (mean age 55.2 ± 9.1 years; n=1,227). For individuals included in this study, gut microbiome 16S rRNA sequencing, musculoskeletal phenotyping derived from DXA images, lifestyle and socioeconomic data, and medication records were available. Per cohort, the 16S rRNA sequencing data, derived from stool, were processed with the DADA2 pipeline and taxonomies were assigned using the SILVA reference database. In addition, the microbiome functional potential was obtained with PICRUSt2. Further, we investigated the association between the human gut microbiome (alpha diversity, genera and predicted functional pathways) and appendicular lean mass (ALM), femoral neck bone mineral density (FN-BMD) and trabecular bone score (TBS) using multilinear regression models controlling for multiple confounders, and performed a joint analysis from both cohorts. Sex-stratified analyses were also conducted.

Results

The gut microbiome alpha diversity was not associated with either tested phenotype after accounting for multiple-testing (P>1.67e-02). In the joint analysis, lower abundance of Oscillibacter (beta= -.51, 95%CI [-0.74, -.29]), Anaerotruncus (beta=-0.41, 95%CI [-0.61, - 0.21]), Eisenbergiella (beta=-0.39, 95%CI [-0.59, -.19]) and higher abundance of Agathobacter (beta=0.40, 95%CI [0.20, 0.60]) were associated with higher ALM (P<2.0e-04). Lower abundance of Anaerotruncus (beta=-0.32, 95%CI [-0.45, -.19]), Hungatella (beta=-0.26, 95%CI [-0.38, -.15]) and Clostridiales bacterium DTU089 (beta=-0.37, 95%CI [-0.55, -.19]) was associated with higher ALM only in females (P< 2.0e-04). Moreover, the biotin biosynthesis II pathway was positively associated with ALM (beta=0.44, 95% CI [0.24, 0.64]) (P<1.90e-04) in females while no associations were observed in males. We did not observe any robust association of bone traits with gut microbiome features.

Conclusion

Our results indicate that specific genera are associated with ALM in middle-aged and older adults and these associations can present in a sex-specific manner. Overall, our study suggests that the gut microbiome is linked to muscle aging in middle-aged and older adults. However, larger sample sizes are still needed to underpin the specific microbiome features involved.

Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism

Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas from Central Africa. Results show that zoo-housed gorillas in the U.S. exhibit the most diverse gut microbiomes and markers of increased protein and carbohydrate fermentation, at the expense of microbial metabolic traits associated with plant cell-wall degradation. Machine learning models identified unique microbial traits in U.S. gorillas with cardiometabolic distress; including reduced metabolism of sulfur-containing amino acids and hexoses, increased abundance of potential enteric pathogens, and low fecal butyrate and propionate production. These findings show that cardiometabolic disease in gorillas is potentially associated with altered gut microbial function, influenced by zoo-specific diets and environments.

Correlating High-dimensional longitudinal microbial features with time-varying outcomes with FLORAL

Correlating time-dependent patient characteristics and matched microbiome samples can be helpful to identify biomarkers in longitudinal microbiome studies. Existing approaches typically repeat a pre-specified modeling approach for all taxonomic features, followed by a multiple testing adjustment step for false discovery rate (FDR) control. In this work, we develop an alternative strategy of using logratio penalized generalized estimating equations, which directly models the longitudinal patient characteristic of interest as the outcome variable and treats microbial features as high-dimensional compositional covariates. A cross validation procedure is developed for variable selection and model selection among different working cor-relation structures. In extensive simulations, the proposed method achieved superior sensitivity over the state-of-the-art methods with robustly controlled FDR. In the analyses of correlating longitudinal dietary intake and microbial features from matched samples of cancer patients, the proposed method effectively identified gut health indicators and clinically relevant microbial markers, showing robust utilities in real-world applications. The method is implemented under the open-source R package FLORAL , which is available at ( https://vdblab.github.io/FLORAL/ ).

Population-level analyses identify host and environmental variables influencing the vaginal microbiome

The vaginal microbiome is critical for the reproductive health of women, yet the differential impacts exerted by the host and by ambient environmental variables on the vaginal microbiome remain largely unknown. Here, we conducted a comprehensive cross-sectional study of the relationships between the vaginal microbiome and 81 matched host and environmental variables across 6755 Chinese women. By 16S rRNA sequencing, we identified four core vaginal microbiota with a prevalence of over 90% and a total median abundance of 98.8%. Twenty-four variables, including physiology, lifestyle behaviors, gynecologic history, social and environmental information, were found associated with the microbiome composition, of which bacterial vaginosis (BV) showed the largest effect size. Age was among the strongest explanatory variables and the vaginal microbiome dynamically succeeded with increasing age, especially with a composition turning point at the age of 45. Our mediation analyses indicated that the effects of age on the microbiome could be mediated by variables such as parity number and lifestyles. We further classified the vaginal microbiomes of the population into 13 "Vagitypes". Women with Lactobacillus iners- and Lactobacillus jensenii-dominated Vagitypes had significantly higher live birth rate than those with Vagitype dominated by Fannyhessea vaginae (53.40%, 59.09% vs 21.43%; OR [95% CI]: 3.62 [1.12-14.87], 5.39 [1.27-27.36]; P = 0.031, P = 0.021). This study provides a comprehensive overview of the associations between identified variables and the vaginal microbiome, representing an important step toward understanding of environment-microbe-host interactions.

Ex vivo oral biofilm model for rapid screening of antimicrobial agents including natural cranberry polyphenols

The search has been ongoing for safe and effective antimicrobial agents for control and prevention of oral biofilm associated with disease. Clinical trials for oral specific anti-bacterials are costly and often provide inconclusive results. The simple approach of ex vivo testing of these agents has not demonstrated utility, likely due to variability of effects observed even with a single donor. We show how shed oral biofilms, easily obtained from donor saliva, and tested under optimized conditions, respond reproducibly to anti-bacterial challenges measured by reductions in rRNA accumulation in susceptible taxa. Responses are in part donor specific, but many bacteria taxa were shown to be reproducibly susceptible over a group of donors. For two antibiotics, vancomycin and penicillin G tested at pharmacologic levels, a subset of Gram-positive bacteria was inhibited. A natural product with antibacterial properties, diluted Vaccinium macrocarpon (cranberry) juice, was shown to inhibit a range of oral taxa, including Alloprevotella sp__HMT_473, Granulicatella adiacens, Lachnoanaerobaculum umeaense, Lepotrichia sp__HMT_215, Peptostreptococcus stomatis, Prevotella nanceiensis, Stomatobaculum sp__HMT_097, Veillonella parvula, and kill some targets. The model discussed in this study has promise as a rapid, precise, and reproducible ex vivo method to test and identify potential clinically useful antimicrobial agents active against the oral biofilm community.

Deciphering the biosynthetic landscape of biofilms in glacier-fed streams

Glacier-fed streams are permanently cold, ultra-oligotrophic, and physically unstable environments, yet microbial life thrives in benthic biofilm communities. Within biofilms, microorganisms rely on secondary metabolites for communication and competition. However, the diversity and genetic potential of secondary metabolites in glacier-fed stream biofilms remain poorly understood. In this study, we present the first large-scale exploration of biosynthetic gene clusters (BGCs) from benthic glacier-fed stream biofilms sampled by the Vanishing Glaciers project from the world's major mountain ranges. We found a remarkable diversity of BGCs, with more than 8,000 of them identified within 2,868 prokaryotic metagenome-assembled genomes, some of them potentially conferring ecological advantages, such as UV protection and quorum sensing. The BGCs were distinct from those sourced from other aquatic microbiomes, with over 40% of them being novel. The glacier-fed stream BGCs exhibited the highest similarity to BGCs from glacier microbiomes. BGC composition displayed geographic patterns and correlated with prokaryotic alpha diversity. We also found that BGC diversity was positively associated with benthic chlorophyll a and prokaryotic diversity, indicative of more biotic interactions in more extensive biofilms. Our study provides new insights into a hitherto poorly explored microbial ecosystem, which is now changing at a rapid pace as glaciers are shrinking due to climate change.

IMPORTANCE

Glacier-fed streams are characterized by low temperatures, high turbidity, and high flow. They host a unique microbiome within biofilms, which form the foundation of the food web and contribute significantly to biogeochemical cycles. Our investigation into secondary metabolites, which likely play an important role in these complex ecosystems, found a unique genetic potential distinct from other aquatic environments. We found the potential to synthesize several secondary metabolites, which may confer ecological advantages, such as UV protection and quorum sensing. This biosynthetic diversity was positively associated with the abundance and complexity of the microbial community, as well as concentrations of chlorophyll a. In the face of climate change, our study offers new insights into a vanishing ecosystem.

Phase I trial comparing bile acid and short-chain fatty acid alterations in stool collected from human subjects treated with omadacycline or vancomycin

Omadacycline, an aminomethylcycline tetracycline, has a low propensity to cause Clostridioides difficile infection (CDI) in clinical trials. Omadacycline exhibited a reduced bactericidal effect compared with vancomycin on key microorganisms implicated in bile acid homeostasis and short-chain fatty acids (SCFAs), key components of CDI pathogenesis. The purpose of this study was to assess bile acid and SCFA changes in stool samples from healthy volunteers given omadacycline or vancomycin. Stool samples were collected daily from 16 healthy volunteers, who were given oral omadacycline or vancomycin for 10 days. Daily stool samples were assessed for bile acids and SCFA concentrations using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Bile acids changed significantly over time for all subjects (P < 0.01 for each bile acid), with vancomycin causing a larger change in the primary bile acids, cholic acid (P < 0.001) and chenodeoxycholic acid (P < 0.001), and a reduced change in the secondary bile acid, lithocholic acid (P < 0.001). The secondary bile acid ursodeoxycholic acid was reduced less by vancomycin than by omadacycline (P < 0.001). All SCFA concentrations were reduced from baseline with a larger effect observed with vancomycin for isobutyric acid (P = 0.0034), propionic acid (P = 0.0012), and acetic acid (P = 0.047). Microbial changes associated with the use of vancomycin versus omadacycline were also associated with changes in bile acid homeostasis and SCFA concentrations. Oral omadacycline produced a distinctive metabolomic profile compared with vancomycin when administered to healthy subjects. The metabolic findings help further our understanding of the lower CDI risk properties of omadacycline and warrant phase 2 investigations using omadacycline as a CDI antibiotic.

IMPORTANCE

The purpose of this study was to assess bile acid and SCFA changes in stool samples obtained from healthy volunteers given omadacycline or vancomycin. Stool samples were collected daily from 16 healthy volunteers given a 10-day oral course of omadacycline or vancomycin. Vancomycin caused a larger change in the primary bile acids and SCFA concentrations compared with omadacycline. The metabolic findings help further our understanding of the mechanistic basis for the lower-risk properties of omadacycline causing CDI and warrant phase 2 investigations using omadacycline as a CDI antibiotic.

CLINICAL TRIALS

This study is registered with ClinicalTrials.gov as NCT06030219.

BioMapAI: Artificial Intelligence Multi-Omics Modeling of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome

Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here, we present BioMapAI, a supervised deep neural network trained on a four-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data, and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and robustly classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct the first connectivity map spanning the microbiome, immune system, and plasma metabolome in health and ME/CFS, adjusted for age, gender, and additional clinical factors. This map uncovers disrupted associations between microbial metabolism (e.g., short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFNγ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing new pathways associated to the disease's heterogeneous symptoms.

Bacterial profiles of the oral, vaginal, and rectal mucosa and colostrum of periparturient sows

The commensal microbiota influences the health, feeding efficiency, and reproductive performance of sows. The microbiota composition in the alimentary and genitourinary tracts and in colostrum/milk during pregnancy and lactation also impacts the microbiota and immune system, growth, and health of the piglets. Knowledge of the microbial compositions is important for evaluation of these effects and for discovering ways to improve the health and productivity of the sows. Oral, vaginal, and rectal mucosa and colostrum were sampled from 32 sows of variable parity in late pregnancy, and colostrum within 6 hours of delivery of the first piglet, on four commercial piglet-producing farms in Finland. Microbial compositions were analyzed by 16S rRNA gene amplicon sequencing. The most abundant genera of the oral microbiota were Rothia, Moraxella, and Streptococcus. The rectal microbiota was dominated by Clostridium sensu stricto 1. Streptococcus was the most abundant genus in the vagina and colostrum. Moderate differences in diversity and composition were observed between farms. The relative abundances of the genera Neisseria (MaAsLin 2 q = 0.002, ANCOMBC q = 0.005), Fusobacterium (MaAsLin 2 q = 0.008, ANCOMBC q = 0.04) and Bacteroides (MaAsLin 2 q < 0.005, ANCOMBC q = 0.06) were lower in oral samples and Romboutsia (MaAsLin 2 q = 0.07, ANCOMBC q = 0.05), Turicibacter (MaAsLin 2 q = 0.08, ANCOMBC q = 0.02) and Lachnospiraceae_UCG_007 (MaAsLin 2 q = 0.1, ANCOMBC q = 0.05) were higher in rectal samples of multiparous compared to primiparous sows. In vaginal samples there was a tendency of higher relative abundances of the genera Fusobacterium and Streptococcus in multiparous than primiparous sows. Among the differentially abundant taxa, F. necrophorum and F. nucleatum were identified in oral samples, F. gastrosuis and F. necrophorum in vaginal samples, and S. dysgalactiae in colostrum samples. This study provides a comprehensive overview of the mucosal and colostrum microbiota of periparturient sows during normal production conditions on Finnish commercial farms.

Gut microbiota dysfunction in Crohn's disease

Introduction

Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.

Methods

We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.

Results

As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.

Conclusions

This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.

Unravelling the hidden side of laundry: malodour, microbiome and pathogenome

BACKGROUND

Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.

RESULTS

Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.

CONCLUSIONS

These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.

Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets

BACKGROUND

Weaning-associated enteric diseases are a major concern in the swine industry. This study investigates the effects of fecal microbiota transplantation (FMT) on the jejunum of weanling piglets, a segment of bowel less studied in terms of microbiomic changes despite its primary involvement in major post-weaning enteric diseases, including postweaning diarrhea (PWD). Thirty-two 3-week-old piglets were divided equally into two groups: Control and FMT. The FMT group received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning. Half of each group was inoculated with an enterotoxigenic E. coli (ETEC) isolate 10 days post-FMT. Piglets were euthanized in the third week (14th and 18th days post-FMT) after weaning to collect intestinal tissues and contents for microbiomic, metabolomic, and transcriptomic analyses.

RESULTS

The jejunal microbiota showed a significant increase in alpha diversity in the third week post-FMT compared with the ileum and colon. FMT significantly enriched the jejunal microbiota composition, while multiple bacterial genera were specifically lacking in control weanling piglets. FMT was strongly associated with the enrichment of the genus Pseudoscardovia of the Bifidobacteriaceae family, which was found lacking in the jejunum of weanling control piglets and inversely associated with the abundance of the genus Bifidobacterium within the same family. Other genera associated with FMT included Solobacterium, Shuttleworthia, and Pseudoraminibacter, whereas bacteria such as Erysipelotrichaceae and Acidaminococcus were identified as most abundant in the control piglets. Metabolomic analysis revealed a significant modulatory effect of FMT on carbohydrate, amino acid, nucleotide, vitamin, and xenobiotic metabolisms, suggesting improved nutrient utilization. Transcriptomic analyses further confirmed the regulatory effects of FMT on gene expression associated with immune, metabolic, barrier, and neuroendocrine functions. Prior FMT treatment in the context of ETEC infection indicated a potential protective role, as evidenced by a significant shift in microbial diversity and metabolomic compositions and decreased diarrhea severity even though no effect on pathogen shedding was evident.

CONCLUSIONS

This study underscores the promise of FMT in enhancing jejunal health. In addition, the results suggest that FMT could be considered a potential strategy to address conditions associated with small intestinal dysbiosis in swine and other monogastric species with similar gut anatomy and physiology, such as humans. Video Abstract.

Modulating the developing gut microbiota with 2'-fucosyllactose and pooled human milk oligosaccharides

BACKGROUND

Synthetic human milk oligosaccharides (HMOs) are used to supplement infant formula despite limited understanding of their impact on the post-weaned developing gut microbiota. Here, we assess the influence of 0.5 g/L 2-fucosyllactose (2'FL) and 4.0 g/L pooled HMOs (pHMOs) on the composition and activity of cultured fecal-derived microbial communities from seven healthy young children.

RESULTS

Exposure to pHMOs induced significant shifts in both the microbial community composition and metabolic output, including an increased abundance of several genera, notably Bacteroides, and the production of health-associated metabolites. In contrast, 2'FL alone did not lead to substantial changes in the communities. A total of 330 bacterial isolates, spanning 157 species, were cultured from these communities and individually evaluated for their responses to HMOs. Over 100 non-Bifidobacterium species showed enhanced growth upon pHMOs treatment and a high degree of intraspecies variation in HMO metabolism was observed.

CONCLUSION

Our study provides valuable insight into the health-enhancing properties of HMOs while highlighting the need for future research into the efficacy of incorporating individual structures into infant formula, particularly when aiming to modulate the gut microbiota. Video Abstract.