DADA2: High-resolution sample inference from Illumina amplicon data

Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease

Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.

Role of insulinemic and inflammatory dietary patterns on gut microbial composition and circulating biomarkers of metabolic health among older American men

Chronic low-grade inflammation and hyperinsulinemia are linked with metabolic dysfunction and dysbiosis. This study investigated the role of dietary inflammatory and insulinemic potential on gut microbiome and circulating health biomarkers in older men. Data from the Osteoporotic Fractures in Men (MrOS) study were analyzed. Reversed Empirical Dietary Inflammatory Pattern (rEDIP), Empirical Dietary Index for Hyperinsulinemia (rEDIH), and Healthy Eating Index (HEI)-2020 scores were computed from food frequency questionnaire data. Stool samples were profiled using 16S rRNA sequencing. Elastic net regression identified diet-associated microbial profiles and multivariable-adjusted linear regression assessed diet-biomarker associations. Higher rEDIP, rEDIH, and HEI-2020 scores were positively associated with gut microbiota alpha diversity. Specific genera, including Intestinibacter and Lachnospira, associated positively, while Dielma, Peptococcus, Feacalitalea, and Negativibaccilus associated inversely with healthier dietary patterns. When evaluating changes in dietary patterns between baseline and visit 4 ( ~ 14 years), these genera tended to define rEDIP, rEDIH more than HEI-2020. In addition, higher dietary quality was linked to better biomarker profiles, including lower creatinine, sodium, triglycerides, and insulin resistance. Beneficial effects of higher dietary quality on health may be mediated by the ability of diet to regulate gut microbial composition and metabolic biomarker profiles.

Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts

Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.

Alterations in mucosa branched N-glycans lead to dysbiosis and downregulation of ILC3: a key driver of intestinal inflammation

The perturbation of the symbiotic relationship between microbes and intestinal immune system contributes to gut inflammation and Inflammatory Bowel Disease (IBD) development. The host mucosa glycans (glycocalyx) creates a major biological interface between gut microorganisms and host immunity that remains ill-defined. Glycans are essential players in IBD immunopathogenesis, even years before disease onset. However, how changes in mucosa glycosylation shape microbiome and how this impact gut immune response and inflammation remains to be clarified. Here, we revealed that alterations in the expression of complex branched N-glycans at gut mucosa surface, modeled in glycoengineered mice, resulted in dysbiosis, with a deficiency in Firmicutes bacteria. Concomitantly, this mucosa N-glycan switch was associated with a downregulation of type 3 innate lymphoid cells (ILC3)-mediated immune response, leading to the transition of ILC3 toward an ILC1 proinflammatory phenotype and increased TNFα production. In addition, we demonstrated that the mucosa glycosylation remodeling through prophylactic supplementation with glycans at steady state was able to restore microbial-derived short-chain fatty acids and microbial sensing (by NOD2 expression) alongside the rescue of the expression of ILC3 module, suppressing intestinal inflammation and controlling disease onset. In a complementary approach, we further showed that IBD patients, often displaying dysbiosis, exhibited a tendency of decreased MGAT5 expression at epithelial cells that was accompanied by reduced ILC3 expression in gut mucosa. Altogether, these results unlock the effects of alterations in mucosa glycome composition in the regulation of the bidirectional crosstalk between microbiota and gut immune response, revealing host branched N-glycans/microbiota/ILC3 axis as an essential pathway in gut homeostasis and in preventing health to intestinal inflammation transition.

Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway

Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.

The intestinal mucosa-associated microbiota in IBD-associated arthritis displays lower relative abundance of Roseburia intestinalis

The most common extra-intestinal manifestation (EIM) of inflammatory bowel disease (IBD), IBD-associated arthritis (IAA), occurs in 25-40% of patients and can be debilitating. In IBD, mucosal and stool microbiota richness is decreased, and compositional changes can precede or accompany disease onset. Likewise, spondyloarthritides are associated with altered gut microbiota, with overlapping bacterial signatures observed in IBD, suggesting key shared microbial factors are involved in both conditions. Much has been learned about the role of the intestinal microbiome in IBD, but less is known regarding its role in IAA. To address this knowledge gap, we analyzed the mucosa-associated intestinal microbiota of participants enrolled in the LOCATION-IBD cohort. Microbiota composition was established using 16S rRNA gene amplicon sequencing of intestinal biopsy samples taken from participants with IBD, with or without arthropathy. Microbiota samples clustered predominantly by participant, and similar taxa were present across the colon. The mucosal intestinal microbiota of females with IAA displayed a lower relative abundance of R. intestinalis, while males with IAA had a higher relative abundance of Corynebacterium, even when controlling for IBD-type, whether samples were taken from a site of inflammation and intestinal location. These findings indicate the mucosa-associated intestinal microbiota is associated with IAA in a sex-specific manner.

Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding

Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.

Unveiling the impact of competition weight loss on gut microbiota: alterations in diversity, composition, and predicted metabolic functions

BACKGROUND

Competitive sports and sports nutrition, popular among amateur athletes aiming for a lean physique, have limited research on gut microbiota.

METHODS

We conducted a 46-week study to analyze the consequences of fat loss and diet restrictions in 23 fitness athletes who prepared for a physique competition. Body composition, dietary intakes, serum cytokines and chemokines, and fecal samples were analyzed.

RESULTS

Fat loss through caloric restriction and aerobic exercise led to an increased phylogenetic diversity of gut microbiota and changes in the composition of gut microbiota, with Faecalibacterium, Lachnospiraceae, Bacteroides, and Intestinimonas showing altered abundances. Fat loss also changed the predicted microbial functions responsible for the metabolism of carbohydrates and amino acids. Consumption of energy, carbohydrates, fiber, vitamins and minerals, and various fatty acids decreased during the preparation for the competition, which was partly associated with changes in gut microbiota. Several cytokine levels decreased (IL1a, IL1b, IL10, and TFNα), and certain chemokine levels increased (GROa and RANTES). During the 23-week regain period after the competition, gut microbiota showed signs of recovery, with increased diversity compared to pre- and post-competition measurements. Most taxonomic changes returned to their baseline levels after the regain period.

CONCLUSIONS

The study highlights the dynamic nature of gut microbiota and its response to fat loss and regain in non-obese fitness/physique competitors and provides novel insights into how competitive sports and sports nutrition can influence the gut ecosystem.

Maternal-infant probiotic transmission mitigates early-life stress-induced autism in mice

Autism, a disorder influenced by both genetic and environmental factors, presents significant challenges for prevention and treatment. While maternal-infant gut microbiota has been a focus in autism research, preventive strategies targeting maternal gut microbiota remain underexplored. This study demonstrates that prenatal probiotic intake can effectively prevent maternal separation-induced autistic-like behaviors in offspring without altering the embryonic neurodevelopment in mice. Using specific PCR primers and cross-fostering experiments, we traced the vertical transmission of probiotics, primarily via fecal/vaginal contamination. Early probiotic colonization conferred resilience against stress-induced gut pathogenic microbes and Th17-mediated peripheral inflammation while significantly inhibiting hypermyelination and neuroinflammation linked to systemic inflammation. Microbial metabolites like tyrosol and xanthurenic acid alleviated neuroinflammation and hypermyelination in vitro, though the causal relationship among neuroinflammation, hypermyelination, and autism in vivo requires further validation. These findings underscore the importance of the maternal-infant microbiota transmission window in autism prevention and highlight the clinical potential of prenatal probiotic interventions.

Systematically-designed mixtures outperform single fibers for gut microbiota support

Dietary fiber interventions to modulate the gut microbiota have largely relied on isolated fibers or specific fiber sources. We hypothesized that fibers systematically blended could promote more health-related bacterial groups. Initially, pooled in vitro fecal fermentations were used to design dietary fiber mixtures to support complementary microbial groups related to health. Then, microbial responses were compared for the designed mixtures versus their single fiber components in vitro using fecal samples from a separate cohort of 10 healthy adults. The designed fiber mixtures outperformed individual fibers in supporting bacterial taxa across donors resulting in superior alpha diversity and unexpected higher SCFA production. Moreover, unique shifts in community structure and specific taxa were observed for fiber mixtures that were not observed for single fibers, suggesting a synergistic effect when certain fibers are put together. Fiber mixture responses were remarkably more consistent than individual fibers across donors in promoting several taxa, especially butyrate producers from the Clostridium cluster XIVa. This is the first demonstration of synergistic fiber interactions for superior support of a diverse group of important beneficial microbes consistent across people, and unexpectedly high SCFA production. Overall, harnessing the synergistic potential of designed fiber mixtures represents a promising and more efficacious avenue for future prebiotic development.

Anxiety-like behavior during protracted morphine withdrawal is driven by gut microbial dysbiosis and attenuated with probiotic treatment

The development of anxiety during protracted opioid withdrawal heightens the risk of relapse into the cycle of addiction. Understanding the mechanisms driving anxiety during opioid withdrawal could facilitate the development of therapeutics to prevent negative affect and promote continued abstinence. Our lab has previously established the gut microbiome as a driver of various side effects of opioid use, including analgesic tolerance and somatic withdrawal symptoms. We therefore hypothesized that the gut microbiome contributes to the development of anxiety-like behavior during protracted opioid withdrawal. In this study, we first established a mouse model of protracted morphine withdrawal, characterized by anxiety-like behavior and gut microbial dysbiosis. Next, we used fecal microbiota transplantation (FMT) to show that gut dysbiosis alone is sufficient to induce anxiety-like behavior. We further demonstrated that probiotic therapy during morphine withdrawal attenuated the onset of anxiety-like behavior, highlighting its therapeutic potential. Lastly, we examined transcriptional changes in the amygdala of morphine-withdrawn mice treated with probiotics to explore mechanisms by which the gut-brain axis mediates anxiety-like behavior. Our results support the use of probiotics as a promising therapeutic strategy to prevent gut dysbiosis and associated anxiety during opioid withdrawal, with potential implications for improving treatment outcomes in opioid recovery programs.

Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential

Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.

Akkermansia muciniphila reverses neuronal atrophy in Negr1 knockout mice with depression-like phenotypes

Genetic predispositions can shape the gut microbiome, which in turn modulates host gene expression and impacts host physiology. The complex interplay between host genetics and the gut microbiome likely contributes to the development of neuropsychiatric disorders, yet the mechanisms behind these interactions remain largely unexplored. In this study, we investigated the gut microbiota in Negr1 knockout (KO) mice, which exhibit anxiety- and depression-like behaviors, as NEGR1 (neuronal growth regulator 1) is a cell adhesion molecule linked to neuronal development and neuropsychiatric disorders. Our findings show significant early-life alterations in the gut microbiota composition of Negr1 KO mice, most notably a marked reduction in Akkermansia spp. along with reduced dendritic arborization and spine density in the nucleus accumbens (NAc) and the dentate gyrus (DG) of the hippocampus. Remarkably, daily administration of an Akkermansia strain isolated from wild-type mice reversed the neuronal structural abnormalities and ameliorated anxiety- and depression-like behaviors in Negr1 KO mice. Transcriptomic profiling revealed upregulation of mitochondrial genome-encoded genes in the NAc and hippocampus of Negr1 KO mice, along with a predisposition toward a pro-inflammatory state in the colon of Negr1 KO mice. The Akkermansia supplementation downregulated these mitochondrial genes in the NAc and hippocampus and upregulated genes involved in T cell activation and immune homeostasis in the colon. These findings demonstrate a novel gene-microbiome interaction in the pathophysiology of Negr1 KO mice, positioning Akkermansia spp. as a key mediator that improves neuronal atrophy and modulates anxiety- and depression-like behaviors. Our study provides compelling evidence for bidirectional interactions between host genetics and the gut microbiome in modulating neuropsychiatric phenotypes, offering new insights for addressing genetically influenced mental disorders.

Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure

The gut microbiome has emerged as a promising target for modulating adverse effects of opioid exposure due to its significant role in health and disease. Opioid use disorder (OUD) has become increasingly prevalent, specifically in women of reproductive age, contributing to an increased incidence of offspring exposed to opioids in utero. Recent studies have shown that prenatal opioid exposure (POE) is associated with notable changes to the maternal gut microbiome, with subsequent implications for the offspring's microbiome and other adverse outcomes. However, the role of the gut microbiome in mediating sex-based differences in pain sensitivity has not yet been investigated. In this study, both male and female C57BL/6 offspring were used to determine sex-based differences in nociception and gut microbial composition as a result of POE. Our data reveals significant sex-based differences in offspring prenatally exposed to opioids. The gut microbiome of opioid-exposed females showed an enrichment of commensal bacteria including Lactobacillus compared to opioid-exposed males. Additionally, POE females demonstrated decreased nociceptive sensitivity, while males demonstrated increased nociceptive sensitivity. RNA sequencing of the prefrontal cortex showed sex-based differences in several canonical pathways, including an increase in the opioid signaling pathway of opioid-exposed females, which was not observed in males. Microbiome modification via maternal probiotic supplementation attenuated sex-based differences throughout the early stages of life. Together, our study provides further insight on sex-based differences arising from POE and highlights the pivotal role of the gut microbiome as a modifiable target for mitigating its negative effects.

Maternal probiotic exposure enhances CD8 T cell protective neonatal immunity and modulates offspring metabolome to control influenza virus infection

Maternal gut microbiota composition contributes to the status of the neonatal immune system and could influence the early life higher susceptibility to viral respiratory infections. Using a novel protocol of murine maternal probiotic supplementation, we report that perinatal exposure to Lacticaseibacillus rhamnosus (L.rh) or Bifidobacterium animalis subsp. lactis (B.lac) increases the influenza A/PR8 virus (IAV) clearance in neonates. Following either supplementation, type 1 conventional dendritic cells (cDC1) were amplified in the lymph nodes leading to an enhanced IAV antigen-experienced IFN-γ producing effector CD8 T cells in neonates and IAV-specific resident memory CD8 T cells in adulthood. This was compatible with a higher protection of the offspring upon a secondary infection. Interestingly, only mice born to L.rh supplemented mothers further displayed an increased activation of IFN-γ producing virtual memory CD8 T cells and a production of IL-10 by CD4 and CD8 T cells that could explain a better control of the lung damages upon infection. In the offspring and the mothers, no disturbance of the gut microbiota was observed but, as analyzed through an untargeted metabolomic approach, both exposures modified neonatal plasma metabolites. Among them, we further demonstrated that genistein and 3-(3-hydroxyphenyl)propionic acid recapitulate viral clearance or cDC1 activation in neonates exposed to IAV. We conclude that maternal L.rh or B.lac supplementation confers the neonates specific metabolomic modulations with a better CD8 T cell-mediated immune protection against IAV infection.

Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans

BACKGROUND

The human gut microbiome-endocannabinoidome axis is crucial for several homeostatic processes, including inflammation and energy metabolism, and is influenced by many endogenous and exogenous factors, such as dietary habits. Changes in the gut microbiome in response to seasonal variations were previously reported and tentatively attributed to shifts in dietary patterns. However, there is a need for longitudinal studies in industrialized populations to comprehensively explore seasonal variations independently of lifestyle confounding factors.

OBJECTIVE

To investigate the longitudinal effects of seasonal variations on the composition of the gut microbiome and the circulating levels of endocannabinoidome mediators in humans, while elucidating the contributing factors underlying these changes.

METHODS

Plasma and fecal samples were collected at the end of both the winter and summer in a longitudinal cohort of 48 individuals living in Québec City (Canada). Dietary habits, medical history, fecal microbiota taxonomic composition and plasma levels of circulating N‑acyl‑ethanolamines (NAEs) and 2‑monoacyl-glycerols (2‑MAGs) were obtained at each time point.

RESULTS

Lower circulating levels of most NAEs were observed at the end of summer. These changes were accompanied by a reduction in the relative abundance of the Bifidobacteriaceae and Lachnospiraceae families, along with an increase in the abundance of the Bacteroidaceae and Ruminococcaceae families. These seasonal variations were not associated with concurrent changes in adiposity parameters, dietary intakes, physical activity habits, or vitamin D status. Importantly, the magnitude of the shift in gut microbiota composition from winter to summer was found to be associated with the seasonal variations in circulating endocannabinoidome (eCBome) mediators.

CONCLUSION

This study identified specific seasonal changes in gut microbiota composition and circulating levels of several NAEs, which were not associated with vitamin D status and lifestyle habits. It underscores the importance of the gut microbiota-endocannabinoidome axis in the pathophysiology of seasonal changes, and of considering seasons in clinical trials on these systems.

Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers

Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.

Training load influences gut microbiome of highly trained rowing athletes

BACKGROUND

Despite the importance of the gut microbiome on physical performance and health, little is known on the impact of training on an athlete's gut health.

OBJECTIVE

This study investigates the effect of training load on markers of gut health.

METHODS

Whole stool (24 h) samples were collected from 23 highly trained rowers (mean ± SD; age 19.2 ± 1.1 y; weight 80.1 ± 11.4 kg; height 1.83 ± 0.09 m) following periods of high (HT) and low training load (LT). The microbiome and short-chain fatty acid concentrations were characterized from the whole stool samples. Three-day weighted food records were used to determine diet quality (ADIcore), macronutrient, and fiber intakes during HT and LT.

RESULTS

By design, training duration (147%) and intensity (130%) were greater during (HT), compared with (LT) (p < 0.001). Carbohydrate, fat, protein, and fiber intake remained stable, but ADIcore was higher in HT (55 ± 10) compared with LT (49 ± 9; t(15) = 2.78, p = 0.014; CI: 1.34 to 10.155). Stool frequency (1.11 ± 0.47 vs 0.67 ± 0.76; p = 0.007) was lower in HT compared with LT, and a greater number of participants were unable to produce a stool sample during LT (8% vs 47%). Short chain fatty acid (SCFA), propionic (120.64 ± 30.06 mm vs 91.35 ± 34.91 mm; p = 0.007), and butyric acid (104.76 ± 50.02 vs 64.23 ± 22.05 mm, p = 0.003) concentrations were lower in HT compared with LT. Alpha diversity, Shannon-Wiener diversity index (3.43 ± 0.37 vs 3.67 ± 0.34, p = 0.09) was lower in HT than LT. The abundance of the dominant Bacteroidia was greater at HT compared to LT and ratio of firmicutes to Bacteroidota (n = 16, 1.31 ± 1.19 vs 4.29 ± 3.88, t(15) = -3.44, p = 0.04, CI = -4.82 to -1.13) was lower in HT compared to LT.

CONCLUSION

Results of this study indicate that gut microbiome, SCFA concentrations, stool frequency, and diet quality vary between periods of high and low training load in athletes. The relationship between these factors and impact of such changes in gut health is currently unclear and warrants further investigation.

MIIST305 mitigates gastrointestinal acute radiation syndrome injury and ameliorates radiation-induced gut microbiome dysbiosis

High-dose radiation exposure results in gastrointestinal (GI) acute radiation syndrome identified by the destruction of mucosal layer, intestinal growth barrier dysfunction, and aberrant inflammatory responses. Further, radiation causes gut microbiome dysbiosis characterized by diminished microbial diversity, mostly commensal bacteria, and the spread of bacterial pathogens that trigger the recruitment of immune cells and the production of pro-inflammatory factors that lead to further GI tissue damage. Currently, there are no U.S. Food and Drug Administration (FDA) approved countermeasures that can treat radiation-induced GI injuries. To meet this critical need, Synedgen Inc. has developed a glycopolymer radiomitigator (MIIST305) that is specifically targeted to the GI tract, which acts by intercalating into the mucus layer and the glycocalyx of intestinal epithelial cells that could potentially ameliorate the deleterious effects of radiation. Male C57BL/6J adult mice were exposed to 13 Gy partial body X-irradiation with 5% bone marrow shielding and MIIST305 was administered on days 1, 3, and 5 post-irradiation. Approximately 85% of the animals survived the irradiation exposure and were apparently healthy until the end of the 30-day study period. In contrast, no control, Vehicle-treated animals survived past day 10 at this radiation dose. We show that MIIST305 improved intestinal epithelial barrier function and suppressed systemic inflammatory responses mediated by radiation-induced pro-inflammatory cytokines. Taxonomic profiling and community structure of the fecal and colonic mucosa microbiota demonstrated that MIIST305 treatment increased microbial diversity and restored abundance of beneficial commensal bacteria, including Lactobacillus and Bifidobacterium genera while suppressing potentially pathogenic bacteria Enterococcus and Staphylococcus compared with Vehicle-treated animals. In summary, MIIST305 is a novel GI-targeted therapeutic that greatly enhances survival in mice exposed to lethal radiation and protects the GI tract from injury by restoring a balanced gut microbiota and reducing pro-inflammatory responses. Further development of this drug as an FDA-approved medical countermeasure is of critical importance.

Gut microbial dysbiosis associated to diarrheic irritable bowel syndrome can be efficiently simulated in the Mucosal ARtificial COLon (M-ARCOL)

Irritable bowel syndrome (IBS) is a common chronic gastrointestinal disorder, with diarrhea-predominant IBS (IBS-D) as the most frequent subtype. The implication of gut microbiota in the disease's etiology is not fully understood. In vitro gut systems can offer a great alternative to in vivo assays in preclinical studies, but no model reproducing IBS-related dysbiotic microbiota has been developed. Thanks to a large literature review, a new Mucosal ARtifical COLon (M-ARCOL) adapted to IBS-D physicochemical and nutritional conditions was set-up. To validate the model and further exploit its potential in a mechanistic study, in vitro fermentations were performed using bioreactors inoculated with stools from healthy individuals (n = 4) or IBS-D patients (n = 4), when the M-ARCOL was set-up under healthy or IBS-D conditions. Setting IBS-D parameters in M-ARCOL inoculated with IBS-D stools maintained the key microbial features associated to the disease in vivo, validating the new system. In particular, compared to the healthy control, the IBS-D model was characterized by a decreased bacterial diversity, together with a lower abundance of Rikenellaceae and Prevotellaceae, but a higher level of Proteobacteria and Akkermansiaceae. Of interest, applying IBS-D parameters to healthy stools was not sufficient to trigger IBS-D dysbiosis and applying healthy parameters to IBS-D stools was not enough to restore microbial balance. This validated IBS-D colonic model can be used as a robust in vitro platform for studies focusing on gut microbes in the absence of the host, as well as for testing food and microbiota-related interventions aimed at personalized restoration of gut microbiota eubiosis.

Mouse strain-specific responses along the gut-brain axis upon fecal microbiota transplantation from children with autism

Several factors are linked to the pathophysiology of autism spectrum disorders (ASD); however, the molecular mechanisms of the condition remain unknown. As intestinal problems and gut microbiota dysbiosis are associated with ASD development and severity, recent studies have focused on elucidating the microbiota-gut-brain axis' involvement. This study aims to explore mechanisms through which gut microbiota might influence ASD. Briefly, we depleted the microbiota of conventional male BALB/cAnNCrl (Balb/c) and C57BL/6J (BL/6) mice prior to human fecal microbiota transplantation (hFMT) with samples from children with ASD or their neurotypical siblings. We found mouse strain-specific responses to ASD hFMT. Notably, Balb/c mice exhibit decreased exploratory and social behavior, and show evidence of intestinal, systemic, and central inflammation accompanied with metabolic shifts. BL/6 mice show less changes after hFMT. Our results reveal that gut microbiota alone induce changes in ASD-like behavior, and highlight the importance of mouse strain selection when investigating multifactorial conditions like ASD.

Single-cell microbiota phenotyping reveals distinct disease and therapy-associated signatures in Crohn's disease

IgA-coated fractions of the intestinal microbiota of Crohn's disease (CD) patients have been shown to contain taxa that hallmark the compositional dysbiosis in CD microbiomes. However, the correlation between other cellular properties of intestinal bacteria and disease has not been explored further, especially for features that are not directly driven by the host immune-system, e.g. the expression of surface sugars by bacteria. By sorting and sequencing IgA-coated and lectin-stained fractions from CD patients microbiota and healthy controls, we found that lectin-stained bacteria were distinct from IgA-coated bacteria, but still displayed specific differences between CD and healthy controls. To exploit the discriminatory potential of both, immunoglobulin coated bacteria and the altered surface sugar expression of bacteria in CD, we developed a multiplexed single cell-based analysis approach for intestinal microbiota. By multi-parameter microbiota flow cytometry (mMFC) we characterized the intestinal microbiota of 55 CD patients and 44 healthy controls for 11-parameters in total, comprising host-immunoglobulin coating and the presence of distinct surface sugar moieties. The data were analyzed by machine-learning to assess disease-specific marker patterns in the microbiota phenotype. mMFC captured detailed characteristics of CD microbiota and identified patterns to classify CD patients. In addition, we identified phenotypic signatures in the CD microbiota which not only reflected remission after 6 weeks of anti-TNF treatment, but were also able to predict remission before the start of an adalimumab treatment course in a pilot study. We here present the proof-of-concept demonstrating that multi-parameter single-cell bacterial phenotyping by mMFC could be a novel tool with high translational potential to expand current microbiome investigations by phenotyping of bacteria to identify disease- and therapy-associated cellular alterations and to reveal novel target properties of bacteria for functional assays and therapeutic approaches.

Mucus-penetrating microbiota drive chronic low-grade intestinal inflammation and metabolic dysregulation

Metabolic syndrome is, in humans, associated with alterations in the composition and localization of the intestinal microbiota, including encroachment of bacteria within the colon's inner mucus layer. Possible promoters of these events include dietary emulsifiers, such as carboxymethylcellulose (CMC) and polysorbate-80 (P80), which, in mice, result in altered microbiota composition, encroachment, low-grade inflammation and metabolic syndrome. While assessments of gut microbiota composition have largely focused on fecal/luminal samples, we hypothesize an outsized role for changes in mucus microbiota in driving low-grade inflammation and its consequences. In support of this notion, we herein report that both CMC and P80 led to stark changes in the mucus microbiome, markedly distinct from those observed in feces. Moreover, transfer of mucus microbiota from CMC- and P80-fed mice to germfree mice resulted in microbiota encroachment, low-grade inflammation, and various features of metabolic syndrome. Thus, we conclude that mucus-associated bacteria are pivotal determinants of intestinal inflammatory tone and host metabolism.

Mucosal washes are useful for sampling intestinal mucus-associated microbiota despite low biomass

Understanding the dynamic relationship between mucus-associated microbiota and host health is critical. However, studies predominantly using stool samples may not accurately represent these bacterial communities. Here, we investigated the mucus-associated microbiota in the gastrointestinal tract of mice and the terminal ileum of humans using different sample types: mucosal washes, brushes, scrapings, and intestinal contents in mice and biopsies, brushes and mucosal washes in humans. We used DNA quantification and 16S rRNA amplicon sequencing to evaluate the comparability of the information yielded from the different sample types under a controlled benchmark. In mice, mucosal washes and brushes had comparative bacterial DNA and host DNA contamination than scraping samples. Similarly, in humans, washes outperformed biopsies in bacterial DNA content. Read counts and microbiota alpha diversity remained remarkably similar in mice and between brushes and washes in humans. The composition of the microbiota varied based on the subsegment and sample type in mice and sample type in humans. We conclude that washes and brushes reduce host contamination without inducing substantial compositional bias when sampling mucosal microbiota. Our findings suggest that mucosal washes and brushes are a viable alternative to biopsies in humans and scrapings in mice, thereby improving the transferability of results across hosts. Our study highlights the importance of focusing on mucus-associated microbiota to better capture host-microbiome interactions at their closer interface.

Multi-species probiotic supplement enhances vagal nerve function - results of a randomized controlled trial in patients with depression and healthy controls

Major depression (MD) significantly impacts individual well-being and society. The vagus nerve plays a pivotal role in the gut-brain axis, facilitating bidirectional communication between these systems. Recent meta-analyses suggest potential antidepressant effects of probiotics, although their mechanisms remain unclear. This study aimed to assess the impact of a multi-species probiotic (OMNi-BiOTiC® STRESS Repair) on vagus nerve function in 43 MD patients and 43 healthy controls (HC). Participants received either probiotics or placebo twice daily. Serum and stool samples were collected at baseline, 7 days, 28 days, and 3 months. Vagus nerve (VN) function was evaluated using 24-hour electrocardiography (ECG) for heart rate variability (HRV), alongside stool microbiome analysis via 16S rRNA sequencing. After 3 months, MD patients receiving probiotics demonstrated significantly improved morning VN function compared to HC. MD participants who were in the probiotic group showed a significant increase in Christensellales, particularly Akkermansia muciniphila along with improved sleep parameters (use of sleep medication, sleep latency) as measured by the Pittsburgh Sleep Quality Inventory (PSI). This study highlights potential physiological benefits of probiotics in MD, potentially mediated through VN stimulation. Understanding these mechanisms could lead to novel therapeutic approaches for MD management.

Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver

Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis (N = 9), Gene-neg adenomatous polyposis (N = 18), and serrated polyposis syndrome (SPS, N = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively. Stool metabolites were quantified via 1H NMR, revealing an increase in alanine in SPS subjects relative to non-polyposis subjects, and Partial Least Squares Discriminant Analysis (PLS-DA) analysis indicated that the proportion of leucine to tyrosine in fecal samples may be predictive of SPS. Use of these microbial and metabolomic signatures may allow for better diagnostric and risk-stratification tools for colonic polyposis patients and their families as well as promote development of microbiome-targeted approaches for polyp prevention.

Novel cross-feeding human gut microbes metabolizing tryptophan to indole-3-propionate

Tryptophan-derived indoles produced by the gut microbiota, particularly indole-3-propionate (IPA), are key compounds associated with gastrointestinal balance and overall health. Reduced levels of IPA have been associated with inflammatory bowel disease, type 2 diabetes, and colorectal cancer. Since fiber-rich diets have been shown to promote IPA, we aimed to decipher fiber-specific effects and identify associated IPA-producing taxa in a range of healthy individuals. We cultured fecal microbiota from 16 adults with tryptophan and eight different dietary fibers and monitored community shifts by 16S rRNA gene amplicon sequencing and tryptophan-derived indoles using targeted liquid chromatography with diode array detection. The concentrations and types of indoles produced were donor-specific, with pectin strongly promoting IPA production in certain donors. IPA production was not associated with any known IPA producer but with the pectin-utilizing species Lachnospira eligens, which produced indole-3-lactate (ILA) in vitro, the IPA precursor. Supplementation of ILA in additional fecal microbiota cultures (n = 6) revealed its effective use as a substrate for IPA production. We identified a novel IPA producer, Enterocloster aldenensis, which produced IPA exclusively from ILA but not from tryptophan. Co-culture of L. eligens and E. aldenensis resulted in IPA production, providing new evidence for an ILA cross-feeding mechanism that may contribute to the IPA-promoting effects observed with pectin. Overall, we highlight the potential for targeted dietary interventions to promote beneficial gut taxa and metabolites.

Distinct gut microbiota and metabolome features of tissue-specific insulin resistance in overweight and obesity

Insulin resistance (IR) is an early marker of cardiometabolic deterioration which may develop heterogeneously in key metabolic organs, including the liver (LIR) and skeletal muscle (MIR). This tissue-specific IR is characterized by distinct metabolic signatures, but the role of the gut microbiota in its etiology remains unclear. Here, we profiled the gut microbiota, its metabolites and the plasma metabolome in individuals with either a LIR or MIR phenotype (n = 233). We observed distinct microbial community structures LIR and MIR, and higher short-chain fatty acid (SCFA) producing bacteria, fecal SCFAs and branched-chain fatty acids and a higher postprandial plasma glucagon-like-peptide-1 response in LIR. In addition, we found variations in metabolome profiles and phenotype-specific associations between microbial taxa and functional metabolite groups. Overall, our study highlights association between gut microbiota and its metabolites composition with IR heterogeneity that can be targeted in precision-based strategies to improve cardiometabolic health. Clinicaltrials.gov registration: NCT03708419.

Vaccine protection of broilers against various doses of wild-type Salmonella Typhimurium and changes in gut microbiota

This study evaluated the impact of vaccine diluents (peptone or water) on the protective effects of Salmonella Typhimurium (S. Typhimurium) vaccine. Vaccinated broilers were challenged with different doses of wild-type S. Typhimurium through dust. At the time of cull, vaccine load was highest in caeca and lowest in spleen. Wild-type S. Typhimurium was detectable after 24 hrs only in the vaccinated birds challenged with 108 CFU and positive control. S. Typhimurium load was lower in the organs of the groups challenged with 104 and 106 compared to the 108 CFU group. The caecal microbiota alpha diversity of the vaccinated or vaccinated and challenged chickens differed from the positive and negative control groups. Beta diversity of the positive control clustered separately from all other treatment groups, showing that vaccine caused minimal changes in gut microbiota structure. The vaccinated and/or wild-type challenged chickens showed significantly higher abundance of Anaerostignum, Lachnoclostridium, Intestinimonas, Colidextribacter, Monoglobus, Acetanaerobacterium and Subdoligranulum. Outcomes from this study demonstrate that the vaccine effectively protected broiler chickens from S. Typhimurium infection and helped maintain a more stable gut microbiota structure, reducing the impact of S. Typhimurium on gut health. Vaccine diluent did not affect gut microbiota composition.

Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis

To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.

Gut microbiome-driven regulation of sex hormone homeostasis: a potential neuroendocrine connection

The gut microbiome is known to have a bidirectional relationship with sex hormone homeostasis; however, its role in mediating interactions between the primary regulatory axes of sex hormones and their productions is yet to be fully understood. We utilized both conventionally raised and gnotobiotic mouse models to investigate the regulatory role of the gut microbiome on the hypothalamic-pituitary-gonadal (HPG) axis. Male and female conventionally raised mice underwent surgical modifications as follows: (1) hormonally intact controls; (2) gonadectomized males and females; (3) gonadectomized males and females supplemented with testosterone and estrogen, respectively. Fecal samples from these mice were used to colonize sex-matched, intact, germ-free recipient mice through fecal microbiota transplant (FMT). Serum gonadotropins, gonadal sex hormones, cecal microbiota, and the serum global metabolome were assessed. FMT recipients of gonadectomized-associated microbiota showed lower circulating gonadotropin levels than recipients of intact-associated microbiota, opposite to that of FMT donors. FMT recipients of gonadectomized-associated microbiota also had greater testicular weights compared to recipients of intact-associated microbiota. The gut microbiota composition of recipient mice differed significantly based on the FMT received, with the male microbiota having a more concerted impact in response to changes in the HPG axis. Network analyses showed that multiple metabolically unrelated pathways may be involved in driving differences in serum metabolites due to sex and microbiome received in the recipient mice. In sum, our findings indicate that the gut microbiome responds to the HPG axis and subsequently modulates its feedback mechanisms. A deeper understanding of interactions between the gut microbiota and the neuroendocrine-gonadal system may contribute to the development of therapies for sexually dimorphic diseases.

Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome

Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.

Strongyle nematode fauna in three ruminants in upper northern Thailand

Gastrointestinal parasites, particularly strongyle nematodes, pose a significant threat to the health of ruminants. Due to the technical limitations of microscopic and conventional PCR-based methods, the strongyle parasite fauna has not been well studied even in common livestock animals. The present study aimed to investigate the prevalence and diversity of strongyle nematodes in three ruminant species in northern Thailand using a nemabiome approach. Fecal samples were collected from buffaloes, cattle, and goats that were raised for meat and for dairy in four provinces in northern Thailand. Strongyle infections were determined using egg flotation and McMaster techniques followed by DNA metabarcoding for species identification. The results showed high prevalence of strongyles especially in goats raised for meat (88 %), and in goats raised for dairy (72 %). Significantly more goats and cattle raised for meat were strongyle egg-positive compared to their dairy counterparts. Notably, deworming frequency was not significantly associated with strongyle egg-positivity in all ruminant groups apart from dairy goats. Nemabiome analysis identified 11 strongyle species across seven genera. Among the ruminant hosts, beef cattle exhibited the highest strongyle richness. Additionally, the dominance of specific strongyle species influenced the differences observed in diversity indices. This research is the first to apply the nemabiome approach to assess strongyle nematode diversity in northern Thailand, providing valuable insights into nematode community compositions. These findings emphasize the importance of molecular techniques for parasite monitoring and the development of targeted control strategies.

Animal farming and the oral microbiome in the Agricultural Health Study

BACKGROUND

Raising farm animals imparts various exposures that may shape the human microbiome. The oral microbiome has been increasingly implicated in disease development. Animal farming has also been associated with certain chronic diseases such as cancer; however, underlying biological mechanisms are unclear. We investigated associations between raising farm animals and the oral microbiome in the Agricultural Health Study.

METHODS

This analysis included 1,245 participants (865 farmers and 380 spouses) who provided oral wash specimens and information on types and numbers of specific animals raised on their farms within 2 years before sample collection. The oral microbiome was measured by sequencing the V4 region of the 16S ribosomal RNA gene. We evaluated associations of farm animal exposures with alpha and beta diversity metrics (within- and between-sample diversity, respectively), as well as presence and relative abundance of specific bacterial genera. All analyses adjusted for potential confounders (e.g., age, sex, smoking, alcohol consumption).

RESULTS

Overall, 63 % of participants raised farm animals, most commonly cattle (46 %) and hogs (20 %). Those who raised a large number of hogs (≥2,000 vs. no hogs) had higher alpha diversity. Conversely, raising sheep/goats and raising larger numbers of poultry were associated with lower alpha diversity. Beta diversity was not significantly different between participants with and without any farm animals. Participants raising any farm animals had higher relative abundance of Porphyromonas and lower relative abundances of Prevotella and Ruminococcaceae UCG-014. Several genera were more likely to be absent with specific animal exposures (e.g., Capnocytophaga for cattle and sheep/goats; Corynebacterium, Dialister, Stomatobaculum, and Solobacterium for sheep/goats and poultry).

CONCLUSIONS

This was the largest study of farm animal exposures and the human microbiome to date. Findings suggest that raising specific farm animals may influence the oral microbiome, supporting the need to further investigate the potential role of animal farming in disease etiology.

Spatial environments of stack and layer shape the quality of Chinese sauce aroma Daqu: Characteristics, functions, and relationships

The Chinese sauce aroma liquor Daqu (CSDQ) is an important raw material and starter in Baijiu processing, which is formed through solid-state fermentation in an open environment. The spatial environment influences the qualities of CSDQ. In this study, the subtypes of CSDQ were defined by types and layers. Based on multiomic methods, the nutrient substances, fermentation-related parameters, flavor compounds, microbial diversity, and bacterial function of different subtypes were comprehensively evaluated. The obtained results revealed that YQ had the most types of characteristic bacteria, WQ provided the most yeast and the highest fermentation power, and BQ had the most pyrazines and Bacillales. The relationships between subtypes or biochemical factors were presented. Trace bacteria exhibited temperate amplification in YQ and BQ, which may be the essential outcome of CSDQs as natural culture mediums. Our findings provided a better understanding of solid-state fermentation in the Baijiu industry.

Metagenomic and meta-metabolomic analysis of traditional Korean rice vinegar productions shows a large variability between producers

Cereal vinegars have been used for thousands of years, especially in Asian countries. These vinegars are still produced in a traditional way by a spontaneous, consecutive, alcoholic and acetic acid fermentation process in open vats under non-sterile conditions, which can lead to an unstable and inconsistent flavor and quality. The present study characterized the microbial diversity of complete, traditional Korean rice vinegar productions at two producers (A and B), from steamed rice to rice vinegar, applying high-throughput amplicon-based and shotgun metagenomic sequencing, in combination with meta-metabolomic analysis. Functional analysis based on metagenome-assembled genomes provided insights into the genetic potential of the different microorganisms involved. Producer A used nuruk, a traditional starter, and seed vinegar to start the alcoholic and acetic acid fermentation phases, respectively, which resulted in highly controlled productions even when different fermentation vessels were used. Producer B used only nuruk to start the vinegar productions, and the spontaneous inoculation of acetic acid bacteria did fail in one of the productions. The addition of nuruk resulted in a simultaneous rice starch saccharification and alcoholic fermentation phase characterized by producer-specific moulds, yeasts, and lactic acid bacteria (LAB). During the acetic acid fermentation phase at both producers (a) novel Acetobacter species, related to A. pasteurianus was found. The simultaneous presence of several LAB species made it hard to link them with the production of specific metabolites. Also, the species contributing to ester formation, important for the flavor, was not clear and requires further research.

Heterogeneous microstructure induces floatation in high-rate anammox granules

The floatation of anammox granules can be a serious challenge in practical wastewater treatment, as it can deteriorate reactor performance and cause bacterial loss. To deepen the understanding of floatation mechanism, in this study, both the floating (F-AnGS) and settling anammox granules (S-AnGS) from a high-rate anammox reactor were comparatively investigated. F-AnGS demonstrated 1.6 times higher specific anammox activity compared to S-AnGS, but only 65 % of produced gas could be successfully released, as quantified by anaerobic respirometry. In addition to the overall EPS accumulation, F-AnGS exhibited a heterogeneous microstructure distinct from that of S-AnGS, as revealed by 3D X-ray microscopic imaging at the single granule level. The heterogeneous distribution of EPS, which can form a dense surface layer, was the main cause for granule floatation. The heterogeneous microstructure of F-AnGS can reduce the distance between microorganisms and enhance the metabolic interaction between anammox bacteria and heterotrophs. The abundance of community members did not have a significant variation, but the functional genes related to anammox and partial denitrification pathway were significantly increased, indicating the enhanced nitrite loop in F-AnGS. This study proposed new structural insights into mechanism of anammox granule floatation, suggesting the appropriate activity control of granule-based anammox process.

Microbiomes of high-rate anaerobic digestors reveal 'Study'-specific factors and limitations of synthetic wastewater

Anaerobic digestion (AD) is a key technology for the treatment of organic wastes and the production of renewable energy. The stability of the process hinges on the underlying microbial populations. Amplicon sequencing is increasingly used to characterise AD microbiomes, yet sequencing efforts have not translated to process engineering of the microbiome or prediction of failure using microbial tools. Using high-rate biofilm wastewater bioreactors as a study system, we aimed to i) discern trends in archaeal and bacterial diversity, ii) identify a core AD microbiome, iii) determine the functional stability of AD microbiomes, and iv) correlate taxa to experimental conditions. We analysed amplicon sequencing data from 32 high-rate anaerobic digestor studies (> 1258 samples) at various operational conditions and applied a suite of statistical microbiome tools. We found that taxonomic archaeal diversity was highly study dependent, while functional diversity was highly shared across studies. A core AD microbiome was identified with > 100 bacterial genera and 6 archaeal genera which were present at > 1 % relative abundance in at least 50 % of samples. Interestingly, we observed that microbiome stability was significantly impacted by the choice of real or synthetic wastewater, with synthetic wastewaters yielding a more stable and less complex microbiome. This was correlated to the abundances of 37 taxa in the synthetic wastewater, including 3 key methanogens (Methanothrix, Methanobacterium, and Methanosphaerula). This suggests that when synthetic wastewater is used in experimental studies, it may not result in an AD microbiome representative of real wastewater treatment systems.

Convergence and divergence of microbial communities in river- Qinghai lake sediment continuum on Tibetan Plateau

Microbiota within interconnected river-lake systems define cycles of carbon and nutrients, yet the mechanisms underlying the assembly of microbial communities during their transition from tributaries to lake remains to be deciphered. This study examined the communities of protists, fungi and bacteria in sediments of Qinghai Lake - a saline lake on the Tibetan Plateau, China - and its connected upstream freshwater tributaries, using high-throughput amplicon sequencing targeting the 18S, ITS2 and 16S rDNA regions. Our findings reveal divergent assembly mechanisms across microbial groups: communities of microeukaryotes (protists and fungi) in tributaries were predominantly shaped by stochastic processes (∼85% contribution), shifting to environmental selection dominance in the lake (∼55%). In contrast, bacterial community assembly in tributaries was primarily deterministic (∼60% environmental selection), shifting to stochastic dominance (∼70%) in the lake. Despite the differences, all groups exhibited congruent biogeographic patterns in terms of diversity and network complexity. The tributary-to-lake transition enhanced the complexity of microbial co-occurrence network but resulted in significant species loss, with α-diversity reduced by 56%-62%. β-diversity increased from tributaries to the estuary but decreased within the lake. Microbial α- and β-diversity correlated positively with sediment C: N ratio but negatively with total sediment C content. Notably, only 1% to 13% of microbial taxa in lake sediments originated from tributaries, suggesting alternative pathways that warrant further geological investigation. This study provides new insights into the convergent biogeographical patterns of diversity and network complexity, coupled with divergent assembly mechanisms, among protist, fungal, and bacterial communities along the river-Qinghai Lake sediment continuum.

Denitrification dominates nitrate attenuation and nitrous oxide effluxes under water table fluctuations

Agricultural soils in riparian zones near rivers often experience frequent water table fluctuations, which can lead to increased nitrogen losses and greenhouse gas emissions via the nitrogen biogeochemical processes. However, the influence of water table fluctuations on the multiple nitrogen transformation processes that dominate nitrate attenuation and nitrous oxide (N2O) effluxes remains poorly understood. In this study, the dynamic changes in depth-dependent nitrate attenuation and soil N2O effluxes, and the responses of microbial communities influenced by water table fluctuations were studied using a series of large column experiments. Our results revealed that dissolved oxygen (DO) concentrations at a depth of -10 cm in sand columns with three different grain sizes (fine→medium→coarse) oscillated, producing oxidizing conditions during drainage and reducing conditions during imbibition periods. DO micro-sensors installed in a layered (sand and sandy loam) column as well as in two sandy loam columns with different regimes in induced water table changes all revealed steady hypoxic conditions. The diversity of the microbial community was significantly correlated with total nitrogen, total organic carbon, and nitrate concentrations, as well as potential denitrification rates. The dominant microbial populations related to the nrfA gene were Methanothrix and Sedimentibacte, whereas those related to denitrification (nirK, nirS, and nosZ) were Pseudomonas and Sulfuricaulis. These findings improve our understanding of the effects of water table fluctuations on groundwater nitrate loss in riparian corridors.

Red mud causes dynamic changes in the soil microbial community and cadmium fractions in a slightly cadmium-contaminated paddy soil

Red mud is a highly alkaline industrial by-product rich in iron oxides with great potential for soil cadmium remediation. Although the stabilization of Cd by red mud is well reported in rice potted and field experiments, the influence of red mud on microbial communities in paddy soil and the contribution of soil microbial communities subjected to red mud in Cd stabilization remain unknown. This study used high-throughput sequencing and bioinformatics, combined with a sequential extraction procedure, to determine the microbiological mechanisms of rice Cd reduction by red mud and information on the corresponding soil Cd fraction. The results showed that red mud significantly increased the soil pH and iron and manganese oxide-bound Cd fractions. Red mud application influenced the microbial beta diversity rather than the alpha diversity, especially for bacteria. Unique taxa associated with iron reduction (e.g., phylum Firmicutes and genus Anaeromyxobacter) were enriched at the rice-filling stage, which may contribute to the stabilization of Cd. Red mud application caused little difference in the fungal communities. A 2 % red mud amendment successfully decreased the grain Cd content in a high Cd-accumulating rice cultivar by 72 %. Red mud effectively reduces Cd accumulation in the short-term and demonstrates potential for remedial applications. This study provides microbiological evidence for stabilizing Cd in red mud, but its long-term environmental impact and field applicability require further research.

Immunopathological and microbial signatures of inflammatory bowel disease in partial RAG deficiency

Partial RAG deficiency (pRD) can manifest with systemic and tissue-specific immune dysregulation, with inflammatory bowel disease (IBD) in 15% of the patients. We aimed at identifying the immunopathological and microbial signatures associated with IBD in patients with pRD and in a mouse model of pRD (Rag1w/w) with spontaneous development of colitis. pRD patients with IBD and Rag1w/w mice showed a systemic and colonic Th1/Th17 inflammatory signature. Restriction of fecal microbial diversity, abundance of pathogenic bacteria, and depletion of microbial species producing short-chain fatty acid were observed, which were associated with impaired induction of lamina propria peripheral Treg cells in Rag1w/w mice. The use of vedolizumab in Rag1w/w mice and of ustekinumab in a pRD patient were ineffective. Antibiotics ameliorated gut inflammation in Rag1w/w mice, but only bone marrow transplantation (BMT) rescued the immunopathological and microbial signatures. Our findings shed new light in the pathophysiology of gut inflammation in pRD and establish a curative role for BMT to resolve the disease phenotype.

Exploring bacterial diversity in Acropora pharaonis: Implications for coral health and growth anomalies

Coral growth anomalies (GA) affect many coral genera across the world, yet the etiology of GAs remains unknown, with limited knowledge of associated bacteria. In this study, we investigated bacterial associations between the growth anomalies (GAs) and healthy (H) portions of coral colonies in Acropora faraonis for two seasons to understand microbial dynamics. Additionally, we examined bacteria in water (W), which could be affecting coral bacterial communities. We found that alpha diversity remained consistent between healthy and GA coral tissues, but their relative abundances differed significantly. Notably, differential analysis revealed the abundance of Endozoicomonas spp., differed significantly between GA and H tissue, although it remains the dominant genus in both GA and H tissue. The high relative abundance of Endozoicomonas spp. in both GA and healthy tissue underscores its potential role in maintaining coral health. Structural modifications in GAs, such as changes in polyp sizes or densities, could be responsible for these differences in bacterial abundance. Similarly, microbial community composition remained consistent between seasons but differed in abundance again. We found differences between microbial communities of GAs and water, but no significant differences were observed between GAs and H, and no previously established bacterial pathogens were detected in GA tissue. These findings describe bacterial community patterns in GAs, but their potential role in its pathogenesis remains unknown. Further metagenomic and meta-transcriptomic analyses are needed to understand potential bacterial involvement in GAs. Additionally, investigating viruses and fungi in GA tissue is recommended to gain deeper insights into GA pathogenesis.

An observational study of the lung microbiome and lung function in young children with cystic fibrosis across two countries with differing antibiotic practices

BACKGROUND

Cystic fibrosis (CF) lung disease begins early, and prophylactic antibiotics have been used to prevent Staphylococcus aureus infection. This study examined the lung microbiome in two countries with differing antibiotic practices and its relationship to lung function in young children with CF.

METHODS

A binational, longitudinal, observational study was performed to define the lower airway microbiome in infants with CF. 16S rRNA sequencing was performed using lavage fluid to characterize the lung microbiota in 45 infants with and without prophylactic antibiotic therapy at an average age of approximately 3 months and 14 months. The association between pulmonary function, bacterial community diversities, and taxa was assessed.

RESULTS

Expected CF bacterial genera and non-traditional bacteria, such as Streptococcus, were identified as core taxa. Microbial community shifts were observed in infants who received antibiotic prophylaxis, with lower alpha diversity (ANOVA, P < 0.05) and a higher proportion of Streptococcus at the first visit. Beta diversity (FEV0.5z; MiRKAT, P < 0.05) and Streptococcus were associated with FEV0.5z (LASSO and linear regression, β < 0). Functional annotation suggested that alteration of lung microbiota may be linked to antimicrobial resistance.

CONCLUSIONS

Lung microbial diversity in infants with CF varied between the two countries, particularly during early infancy. A shift in the lung microbiome toward a higher relative abundance of Streptococcus was associated with reduced pulmonary function.

Investigating the role of primary fungi in Huangjiu fermentation: Insights from flavor orientation and synthetic microbiomes

Huangjiu, a traditional alcoholic beverage, presents a complex fermentation ecosystem primarily influenced by specific fungal species. This study utilized a culture-dependent approach and amplicon sequencing to explore fungal community succession during Huangjiu fermentation. Key fungi identified include Saccharomyces cerevisiae, Aspergillus species (flavus, oryzae, niger), Saccharomycopsis fibuligera, Thermomyces lanuginosus, Rhizopus arrhizus, Issatchenkia orientalis, Wickerhamomyces anomalus, and Diutina rugosa. Employing a synthetic microbiome, we developed a dual-strain fermentation system to evaluate the impact of these fungi on Huangjiu's organoleptic properties. Introduction of these fungi significantly altered the flavor profile, enhancing 23 volatile organic compounds (VOCs), with S. fibuligera notably increasing nine distinct VOCs. While molds contributed to bitterness by increasing bitter amino acids, S. fibuligera effectively mitigated these components, enhancing the beverage's alcohol body, smoothness, and balance. These findings provide crucial insights for optimizing Huangjiu fermentation to improve its quality and appeal.

Light/dark cycles and iron supplementation to enhance the simultaneous production of polyhydroxyalkanoates, 5-aminolevulinic acid, coenzyme Q10, and pigments through photofermentation

This study aimed to obtain 5-aminolevulinic acid (5-ALA), Coenzyme Q10 (CoQ10), polyhydroxyalkanoates (PHA), carotenoids, and bacteriochlorophylls (Bchl) through the photofermentation of residual wine lees. Light/dark cycles and iron supplementation were evaluated. Under 12-hour light/dark cycles, the production of 5-ALA, CoQ10, carotenoids, and Bchl increased by 1.7, 2.8, 1.7, and 2.4 times, respectively, compared to the continuous illumination control, while PHA production decreased from 511 to 445 mg/L. Combining light/dark cycles with iron supplementation enhanced the biomass production rate. The CoQ10 content increased by 4.9 times (reaching 8.8 mg/g-dw), carotenoids by 3.7 times (6.4 mg/g-dw), and Bchl by 6.4 times (17.9 mg/g-dw) compared to the control treatment, while maintaining 5-ALA at 5.3 µmol/L and PHA at 377 mg/L. The combination of light/dark cycles and iron provides a triple benefit: increased production of value-added substances, enhanced biomass production rate, and improved organic matter removal, making it an attractive option for winery effluent treatment and valorization.

Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer

Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.

Identification of specific gut microbes and their therapeutic potential in ameliorating systemic lupus erythematosus in a mouse model

AIMS

The gut microbiome significantly influences autoimmune diseases, including systemic lupus erythematosus (SLE). This study aimed to characterize the gut microbiome and metabolome in SLE and evaluate the therapeutic potential of specific microbial supplementation in MRL/lpr mice.

MATERIALS AND METHODS

MRL/lpr mice, a well-established model for SLE, were used to analyze gut microbiome changes before and after SLE symptom onset. 16S rRNA sequencing and GC-MS-based metabolic profiling were performed to identify key microbial species and associated metabolites. Selected microbes were supplemented in MRL/lpr mice for 10 weeks, and their effects on SLE symptoms and Th17/Treg balance were evaluated.

KEY FINDINGS

Eisenbergiella massiliensis, Lacrimispora saccharolytica, and Hungatella xylanolytica were significantly decreased in MRL/lpr mice following the onset of SLE symptoms. These microbes were strongly correlated with specific metabolites, including 5-cholestanol, cholesterol, p-cresol, and indole. Supplementation with these microbes alleviated SLE symptoms and modulated the Th17/Treg balance.

SIGNIFICANCE

This study highlights the critical role of gut microbiota in immune regulation and SLE symptom relief. Targeted microbial supplementation may serve as a novel therapeutic strategy for managing SLE.

Anaerobic digestion at high-pH and alkalinity for biomethane production: Insights into methane yield, biomethane purity, and process performance

The role of high-pH conditions in anaerobic digestion (AD) has traditionally been confined to it's use in pre-treatment processes. However, operating AD at elevated pH and alkalinity offers significant advantages, including in-situ upgrading of biogas to biomethane. This study examines the potential and scalability of AD under these conditions (pH ∼ 9.3; alkalinity ∼ 0.5 eq/L). The substrate used was the alkaline waste generated from the extraction of extracellular polymeric substances (EPS) from aerobic granular sludge (AGS), and the inoculum used was a haloalkaliphile microbial community from soda lake sediments. To evaluate the system's performance, the organic loading rate (OLR) was incrementally increased. The highest methane production obtained was 8.4 ± 0.1 mL/day/gVSadded at a hydraulic retention time (HRT) of 15 days and an OLR of 1 kgVS/day/m3. At this loading rate, methanogenesis became the rate limiting conversion. The maximum volatile solids conversion was 48.1 ± 1.1 %. Throughout the reactor operation, methane purity in the biogas consistently exceeded 90 % peaking at 96.0 ± 0.2 %, showcasing the potential for in-situ biogas purification under these conditions. In addition, no ammonia inhibition was observed, even with free-ammonia (NH3) concentrations reaching up to 14 mM. This study underscores the potential of high-pH anaerobic digestion as a sustainable method for both waste treatment and energy recovery.

An approach for quantifying the influence of fish farm waste on hard-bottom habitats

Sea-based fish farms release significant quantities of fish feaces, waste feed and associated contaminants into the surrounding environment, necessitating ecological effects-based monitoring. Traditionally, this has been achieved by measuring geochemical and biological properties of sediments obtained by a benthic grab. However, many modern high-capacity farms are situated over hard substrates, rendering conventional sampling methods ineffective and hindering environmental management. Fortunately, new possibilities have emerged with the advent of high-throughput sequencing, and in-particular, the use of microbial eDNA as an indicator of benthic enrichment, and new methods have been developed for obtaining the source material irrespective of substrate. Here, we first demonstrate how applying the default approach used by the world's largest salmon farming industry to hard substrates is essentially qualitative and can lead to inappropriate conclusions. We then show the results from a substrate independent benthic sampling (SIBS) method coupled with a structured quantitative visual assessment of seabed images. The approach utilizes three novel indicators that quantify the degree of visual organic loading (VOL) and ecological effects (VEE) and elucidate the magnitude and spatial extent of the waste influence field via an index (bMBI) derived from 16S eDNA. VOL and VEE were useful for quantifying and classifying effects beneath farms, but were of limited use further away, whereas the bMBI was both highly quantitative and sensitive in the immediate and more distant receiving environments. This dual approach provides a basis for the development of a quantitative hard-bottom monitoring system and should therefore permit effective environment management in the future.