Multivariable association discovery in population-scale meta-omics studies

The microbiota-derived bile acid taurodeoxycholic acid improves hepatic cholesterol levels in mice with cancer cachexia

Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.

Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode

Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.

Machine-learning assisted discovery unveils novel interplay between gut microbiota and host metabolic disturbance in diabetic kidney disease

Diabetic kidney disease (DKD) is a serious healthcare dilemma. Nonetheless, the interplay between the functional capacity of gut microbiota and their host remains elusive for DKD. This study aims to elucidate the functional capability of gut microbiota to affect kidney function of DKD patients. A total of 990 subjects were enrolled consisting of a control group (n = 455), a type 2 diabetes mellitus group (DM, n = 204), a DKD group (n = 182) and a chronic kidney disease group (CKD, n = 149). Full-length sequencing of 16S rRNA genes from stool DNA was conducted. Three findings are pinpointed. Firstly, new types of microbiota biomarkers have been created using a machine-learning (ML) method, namely relative abundance of a microbe, presence or absence of a microbe, and the hierarchy ratio between two different taxonomies. Four different panels of features were selected to be analyzed: (i) DM vs. Control, (ii) DKD vs. DM, (iii) DKD vs. CKD, and (iv) CKD vs. Control. These had accuracy rates between 0.72 and 0.78 and areas under curve between 0.79 and 0.86. Secondly, 13 gut microbiota biomarkers, which are strongly correlated with anthropometric, metabolic and/or renal indexes, concomitantly identified by the ML algorithm and the differential abundance method were highly discriminatory. Finally, the predicted functional capability of a DKD-specific biomarker, Gemmiger spp. is enriched in carbohydrate metabolism and branched-chain amino acid (BCAA) biosynthesis. Coincidentally, the circulating levels of various BCAAs (L-valine, L-leucine and L-isoleucine) and their precursor, L-glutamate, are significantly increased in DM and DKD patients, which suggests that, when hyperglycemia is present, there has been alterations in various interconnected pathways associated with glycolysis, pyruvate fermentation and BCAA biosynthesis. Our findings demonstrate that there is a link involving the gut-kidney axis in DKD patients. Furthermore, our findings highlight specific gut bacteria that can acts as useful biomarkers; these could have mechanistic and diagnostic implications.

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.

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic morphine

The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for drug dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance, which could be influenced by differences in microbiota, and yet no study design has capitalized upon this natural variation. We leveraged natural behavioral variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained sustained antinociception. Mice that did not develop tolerance maintained a higher capacity for production of the short-chain fatty acid (SCFA) butyrate known to bolster intestinal barriers and promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor mice that did not develop tolerance and dietary butyrate supplementation significantly reduced the development of tolerance independently of suppression of systemic inflammation. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

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.

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.

Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19

Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.

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.

A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease

Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.

Nitrate supplementation affects taste by changing the oral metabolome and microbiome

Nitrate, an inorganic anion found in various foods is also present in saliva and has emerged as a potential prebiotic for the oral microbiome. Salivary glands concentrate nitrate from the bloodstream and release it into the oral cavity via the anion transporter sialin SLC17A5. In previous studies dietary nitrate supplementation altered oral bacteria composition, favouring genera like Rothia and Neisseria while reducing Streptococcus, Veillonella, Prevotella, and Actinomyces. The present study hypothesized that taste intensity might adapt to changes in the oral microbiome caused by nitrate supplementation. Participants underwent taste tests before, during, and after supplementation. All subjects showed greater levels of salivary nitrate during supplementation and had higher levels of Neisseria compared to before. Subjects were then grouped according to taste tests (before vs. during) as responders (ANOVA p < 0.05, n = 7), and non-responders (ANOVA p > 0.05, n = 6) and their salivary metabolome and oral microbiome further analysed. Responders had significantly less 5-amino pentanoate, formate, propionate and butyrate in saliva while non-responders showed no metabolite changes between before and during supplementation. In contrast, non-responders had increased Capnocytophaga gingivalis and altered lysosomal degradation pathways. Overall, nitrate supplementation shifted the oral microbiome composition in all subjects and when taste intensity was altered this correlated to bacteria-derived short-chain fatty acid production. This suggests taste perception is affected by the oral microbiome.

Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems

The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.

Alterations of early-life gut microbiome in hospitalized infants with chemical pollutants exposure

Exposure to chemical pollutants and their effects on the gut microbiome during early life are scarce, especially the effects of mixed exposures. Plasma pollutants levels were measured using gas chromatography -triple quadrupole mass spectrometer (GC-MS/MS) among 304 infants in the neonatal ward at Hunan Children's hospital, China, and gut microbiota was derived from 16S rRNA sequencing. We assessed exposure and alpha diversity using generalized linear models, and variation in beta diversity (Bray-Curtis), taxa abundance (MaAsLin2), and employed Bayesian kernel machine regression (BKMR) to investigate the association of pollutants mixture with alpha diversity and taxa. PBDE-99 was positively associated with the Chao1 index (β = 4.29, 95%CI:1.54,7.03). Exposure to the pesticides trifluralin, γ-BHC, and methidathion significantly affected beta diversity (all PFDR < 0.05). PBDE-100, β-BHC, phosalone, methiamitron, fenpropathrin, δ-BHC, and o,p'-DDT were associated with changes in taxa abundance, including negative associations [e.g., Staphylococcus, Bacteroides, Bifidobacterium, and Corynebacterium] and positive associations [e.g., Acinetobacter and Pseudomonas]. An interaction between o,p'-DDT and δ-BHC on Pseudomonas was also found in BKMR models. Our findings suggest that chemical pollutants are associated with gut microbiome changes in hospitalized infants, providing new insights into the mechanisms of chemical pollutants toxicity. Further validation is necessary to confirm these associations and explore their long-term health effects.

A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design

BACKGROUND

The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.

METHODS

We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.

RESULTS

Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.

CONCLUSION

The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.

The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo

Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.

Interactions of erythromycin and an antibiotic mixture with the gut microbiome of juvenile rainbow trout

Erythromycin (ERY) is a commonly used antibiotic found in wastewater effluents and the environment globally. Due to the bioactivity by which they kill and prevent bacterial growth, ERY and other antibiotics may have significant unwanted impacts on the gut microbiome of fishes. The overall objective of this project was to assess effects on the gut microbiome in response to exposure to ERY alone or in a mixture with other common antibiotics, which was accomplished in two experiments. The objectives of experiment 1 as a pilot study were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7-d exposure to three concentrations of ERY followed by a 7-d depuration period. Furthermore, throughout the study changes in gut microbiome were assessed. In experiment 2, an identical experimental design was used to assess the effects of a mixture of antibiotics containing, in addition to ERY, 100 μg/g each of ampicillin, metronidazole, and ciprofloxacin. In that study, three matrices were analyzed, with gut collected for 16S rRNA metabarcoding, blood plasma for non-targeted metabolomics, and brain tissue for mRNA-seq analysis. ERY was relatively quickly depurated from fish and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7-d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing distinct temporal dynamics compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. The transcriptome of the brain was only slightly altered due to antibiotic exposure. Results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics present in fish feed and the environment, with implications for host health.

Biodiversity of the Bacterial and Fungal Microbiome and Associated Inflammatory Cytokine Profile in Chronic Rhinosinusitis

BACKGROUND

Dysbiosis of the bacterial and fungal microbiome has been increasingly implicated in the pathogenesis of chronic rhinosinusitis (CRS). This study explores the relationship between microbiome and mycobiome biodiversity and type 2 (T2) versus non-type 2 (NT2) inflammation.

METHODS

Mucosal tissues from the ethmoid sinus were collected during endoscopic sinus (CRS) and skull base (controls) surgery between January 2020 and July 2021. Specimens underwent 16S rRNA (bacterial) and internal transcribed spacer (fungal) gene sequencing, along with cytokine analysis using the Luminex assay. Based on cytokine (IL-4, IL-5, IL-13) concentrations and the presence of eosinophils, CRS cases were classified into T2 or NT2 inflammatory profiles. The relationships between CRS endotype and the biodiversity of the microbiome and mycobiome were assessed.

RESULTS

Specimens from 92 patients (30 control, 31 CRSwNP, 31 CRSsNP) were included in the analyses. Among 62 CRS cases, 20 exhibited T2 inflammation and 42 exhibited NT2 inflammation. Compared with control specimens, NT2 specimens exhibited significantly lower amplicon sequence variants (mean difference -149, 95% CI [-261, -37], p = 0.007), Shannon index (-0.48 [-0.79, -0.16], p = 0.002), and Simpson index (-0.003 [-0.005, -0.001], p = 0.002) for bacterial alpha diversity. However, no significant differences in bacterial alpha diversity were observed between T2 specimens and controls, or between T2 and NT2 specimens. Fungal biodiversity did not differ significantly across endotype and control groups.

CONCLUSION

Dysbiosis of the sinus bacterial microbiome is more strongly associated with a NT2-mediated inflammatory profile than with a T2-mediated inflammatory profile.

Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders

BACKGROUND

Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.

RESULTS

Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.

CONCLUSION

We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.

Dynamics of the gut microbiome in subjects challenged with Shigella sonnei 53G in a controlled human infection model

Shigella is a significant cause of diarrhea, predominantly affecting children in low- and middle-income countries, as well as international travelers. Not all individuals exposed to Shigella or other enteropathogens have symptomatic responses, and investigating the differences between symptomatic and asymptomatic individuals can further our understanding of enteropathogen proliferation and symptomatic responses. Here, we profiled the fecal microbiomes of 45 individuals infected with Shigella sonnei strain 53G through 16S rRNA sequencing in a controlled human infection model before and during infection, after antibiotic treatment, and after clinical recovery. This model allowed for a detailed exploration of microbiome temporal dynamics during infection, as well as a comparative analysis between those with shigellosis (defined as severe symptoms caused by Shigella infection, including severe diarrhea, fever, and/or abdominal pain) and those without shigellosis. Alpha diversity decreased to a greater degree in individuals with shigellosis. Perturbations in microbial composition during infection and antibiotic treatment were significantly larger in individuals diagnosed with shigellosis than in those who were not. Participants with shigellosis had persistent changes to their microbiomes after recovery, while those without shigellosis recovered to a composition resembling their pre-infection microbiomes. These persistent changes included taxa associated with gut inflammation, such as a decrease in Faecalibacterium and an increase in Ruminococcus gnavus. Furthermore, the initial microbiomes of participants who did not develop shigellosis had a greater abundance of taxa associated with short-chain fatty acid production than participants who did develop shigellosis, including Bifidobacterium, Roseburia, and Faecalibacterium. These data could help prevent Shigella infection or symptoms.IMPORTANCEDiarrheal disease is a major contributor to the global disease burden and can lead to an increased individual risk of chronic sequelae post-infection, such as irritable bowel syndrome, reactive arthritis, and altered gut permeability. Understanding the differential responses of individuals to enteropathogen exposure can elucidate factors that could lead to treatments or preventative measures to reduce the disease burden. Here, we use a controlled human infection model study to directly identify the effects of Shigella sonnei 53G infection on the microbiome. We identified taxa that were more or less abundant in participants who would develop shigellosis during the study, as well as persistent changes after recovery in the microbiomes of participants who developed severe symptoms. Understanding these changes could elucidate ways to prevent Shigella infection or recover altered microbiomes after recovery.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT02816346.

Multi-omics approach identifies gut microbiota variations associated with depression

The gut microbiota plays a potential role in the pathophysiology of depression through the gut-brain axis. This cross-sectional study in 400 participants from the PREDIMED-Plus study investigates the interplay between gut microbiota and depression using a multi-omics approach. Depression was defined as antidepressant use or high Beck Depression Inventory-II scores. Gut microbiota was characterized by 16S rRNA sequencing, and faecal metabolites were analysed via liquid chromatography-tandem mass spectrometry. Participants with depression exhibited significant differences in gut microbial composition and metabolic profiles. Differentially abundant taxa included Acidaminococcus, Christensenellaceae R-7 group, and Megasphaera, among others. Metabolomic analysis revealed 15 significantly altered metabolites, primarily lipids, organic acids, and benzenoids, some of which correlated with gut microbial features. This study highlights the interplay between the gut microbiota and depression, paving the way for future research to determine whether gut microbiota influences depression pathophysiology or reflects changes associated with depression.

Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial

This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.

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.

Fecal Microbiome Reflects Disease State and Prognosis in Inflammatory Bowel Disease in an Adult Population-Based Inception Cohort

INTRODUCTION

We aimed to determine the diagnostic and prognostic potential of baseline microbiome profiling in inflammatory bowel disease (IBD).

METHODS

Participants with ulcerative colitis (UC), Crohn's disease (CD), suspected IBD, and non-IBD symptomatic controls were included in the prospective population-based cohort Inflammatory Bowel Disease in South-Eastern Norway III (third iteration) based on suspicion of IBD. The participants donated fecal samples that were analyzed with 16S rRNA sequencing. Disease course severity was evaluated at the 1-year follow-up. A stringent statistical consensus approach for differential abundance analysis with 3 different tools was applied, together with machine learning modeling.

RESULTS

A total of 1404 individuals were included, where n = 1229 samples from adults were used in the main analyses (n = 658 UC, n = 324 CD, n = 36 IBD-U, n = 67 suspected IBD, and n = 144 non-IBD symptomatic controls). Microbiome profiles were compared with biochemical markers in machine learning models to differentiate IBD from non-IBD symptomatic controls (area under the receiver operating curve [AUC] 0.75-0.79). For UC vs controls, integrating microbiome data with biochemical markers like fecal calprotectin mildly improved classification (AUC 0.83 to 0.86, P < .0001). Extensive differences in microbiome composition between UC and CD were identified, which could be quantified as an index of differentially abundant genera. This index was validated across published datasets from 3 continents. The UC-CD index discriminated between ileal and colonic CD (linear regression, P = .008) and between colonic CD and UC (P = .005), suggesting a location-dependent gradient. Microbiome profiles outperformed biochemical markers in predicting a severe disease course in UC (AUC 0.72 vs 0.65, P < .0001), even in those with a mild disease at baseline (AUC 0.66 vs 0.59, P < .0001).

CONCLUSIONS

Fecal microbiome profiling at baseline held limited potential to diagnose IBD from non-IBD compared with standard-of-care. However, microbiome shows promise for predicting future disease courses in UC.

Association between maternal stress patterns and neonatal meconium microbiota: A prospective cohort study

BACKGROUND

This study aimed to identify maternal stress patterns and investigate their associations with neonatal meconium microbiota.

METHODS

A total of 465 pregnant women reported their stress conditions, including depression, anxiety, pregnancy-related anxiety, perceived stress, sleep, fear of birth, life events, and adverse childhood experiences. Meconium samples were collected from 348 newborns. Latent class analysis was used to identify the patterns of maternal stress.

RESULTS

Three group profiles were identified: "high negative emotion," "high ACEs-low negative emotion," and "low stress." the high ACEs-low negative emotion group and low stress group had higher levels of Chao1 diversity than the high negative emotion group (B = 0.25, P < 0.001; B = 0.18, P < 0.001, respectively). The high ACEs-low negative emotion group had higher levels of Chao1 diversity than the low stress group (B = 0.08, P = 0.001). The variations were observed in the abundance of Bacteroidetes, unidentified_Muribaculaceae, unclassified_Lachnospiraceae, unclassified_Clostridiales, unidentified_Bacteroidales, Oscillospira, and Ruminococcus among different maternal stress patterns.

LIMITATIONS

We did not analyze maternal microbiome samples and assessed the gut microbiota at only one time point.

CONCLUSIONS

These findings emphasized the need for a comprehensive approach to prenatal care that extends beyond traditional medical interventions. Addressing maternal stress through targeted support and interventions may help newborns benefit from a more favorable gut microbiota landscape.

Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility

The goal of this study was to analyze the microbial profiles of meat and contact surfaces from two different processing lines in a pork processing plant, using a 16S rRNA gene amplicon sequencing workflow specifically designed to investigate fresh meat and environmental samples throughout a commercial production schedule. Results indicated that the microbiota differed between the meat and contact surface, both across the two processing lines and within each individual processing line. Differences in the microbiota composition were also strongly associated with both the specific processing dates and the time of day during processing. Much of this variation was associated with distinct amplicon sequence variants unique to each processing date and each processing line throughout the day. The abundance of key taxa associated with food safety and spoilage was also temporally dynamic across a production shift and was different between the meat and contact surface. Overall, the results of this study indicate significant differences in the microbial profiles of the meat and contact surfaces between two processing lines within the same plant. These differences are likely influenced by daily variation in processing and sanitation procedures, as well as differences in the design of the processing lines, which appear to affect the microbiotas of both the meat and contact surfaces.IMPORTANCEThis study provides critical knowledge that can be used as a foundation for tailored processes to improve fresh pork safety and quality, potentially customized to individual processing lines, time points within a shift, and/or production days. Additionally, this study provides a list of potential biological markers associated with food safety and quality that could be used by processors to develop and validate intervention strategies specific to different processing lines.

The link between ultra-processed food consumption, fecal microbiota, and metabolomic profiles in older mediterranean adults at high cardiovascular risk

BACKGROUND

Ultra-processed food (UPF) consumption has been linked to adverse metabolic outcomes, potentially mediated by alterations in gut microbiota and metabolite production.

OBJECTIVE

This study aims to explore the cross-sectional and longitudinal associations between NOVA-classified UPF consumption, fecal microbiota, and fecal metabolome in a population of Mediterranean older adults at high cardiovascular risk.

METHODS

A total of 385 individuals, aged between 55 and 75 years, were included in the study. Dietary and lifestyle information, anthropometric measurements, and stool samples were collected at baseline and after 1-year follow-up. Fecal microbiota and metabolome were assessed using 16 S rRNA sequencing and liquid chromatography-tandem mass spectrometry, respectively.

RESULTS

At baseline, higher UPF consumption was associated with lower abundance of Ruminococcaceae incertae sedis (β = - 0.275, P = 0.047) and lower concentrations of the metabolites propionylcarnitine (β = - 0.0003, P = 0.013) and pipecolic acid (β = - 0.0003, P = 0.040) in feces. Longitudinally, increased UPF consumption was linked to reduced abundance of Parabacteroides spp. after a 1-year follow-up (β = - 0.278, P = 0.002).

CONCLUSIONS

High UPF consumption was associated with less favorable gut microbiota and metabolite profiles, suggesting a possible link to reduced short-chain fatty acid (SCFA) production, altered mitochondrial energy metabolism, and impaired amino acid metabolism. These findings support the reduction of UPF consumption and the promotion of dietary patterns rich in fiber for better gut health. Further research is needed to confirm these associations and clarify the underlying mechanisms.

TRIAL REGISTRATION

ISRCTN89898870 ( https://doi.org/10.1186/ISRCTN89898870 ).

Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres

Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.

Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken

Diet has been reported to impact the diversity and function of gut microbiota. Our study investigated the effect of dietary fat types on cecal microbial composition and predicted function in broiler chickens at days 41 and 55 of age. Four dietary fat sources were evaluated and compared to a control dietary fat source of poultry fat. These were for two diets rich in omega-3 polyunsaturated fatty acids (PUFA) - fish oil and flaxseed oil, a diet rich in long-chain saturated fatty acid (SFA) - lard, and a diet rich in medium-chain saturated fatty acid - coconut oil. At day 55, broiler chickens fed a PUFA-rich diet maintained cecal microbial diversity while broiler chickens fed a SFA-rich diet exhibited a significant reduction in diversity compared to the control diet-fed chickens. More specifically, PUFA intake was associated with elevated levels of microbial carbohydrate metabolizing capability, contributing to efficient energy utilization and enhanced short-chain fatty acid production capability. In contrast, SFA-rich diets lowered abundances for key microbial families like Lachnospiraceae and Bifidobacteriaceae hampering nutrient digestibility and pathogen resistance. The microbiomes for chickens fed lard and coconut oil diets showed a significant reduction in SCFA-producing microbial taxa abundance while the microbial functional profile indicated reduced carbohydrate metabolism. Our findings underscore the contrasting effects of SFA-rich fat and PUFA-rich fat on the cecal microbiota of broiler chickens. The results suggest that incorporating PUFA-rich dietary fats into broiler feed may offer potential benefits by modulating the cecal gut microbiota toward outcomes associated with elevated carbohydrate utilization without hampering nutrient digestibility and pathogen resistance.

Fecal profiling reveals a common microbial signature for pancreatic cancer in Finnish and Iranian cohorts

BACKGROUND

Pancreatic cancer (PC) presents a significant challenge in oncology because of its late-stage diagnosis and limited treatment options. The inadequacy of current screening methods has prompted investigations into stool-based assays and microbial classifiers as potential early detection markers. The gut microbiota composition of PC patients may be influenced by population differences, thereby impacting the accuracy of disease prediction. However, comprehensive profiling of the PC gut microbiota and analysis of these cofactors remain limited. Therefore, we analyzed the stool microbiota of 33 Finnish and 50 Iranian PC patients along with 35 Finnish and 34 Iranian healthy controls using 16S rRNA gene sequencing. We assessed similarities and differences of PC gut microbiota in both populations while considering sociocultural impacts and generated a statistical model for disease prediction based on microbial classifiers. Our aim was to expand the current understanding of the PC gut microbiota, discuss the impact of population differences, and contribute to the development of early PC diagnosis through microbial biomarkers.

RESULTS

Compared with healthy controls, PC patients presented reduced microbial diversity, with discernible microbial profiles influenced by factors such as ethnicity, demographics, and lifestyle. PC was marked by significantly higher abundances of facultative pathogens including Enterobacteriaceae, Enterococcaceae, and Fusobacteriaceae, and significantly lower abundances of beneficial bacteria. In particular, bacteria belonging to the Clostridia class, such as butyrate-producing Lachnospiraceae, Butyricicoccaceae, and Ruminococcaceae, were depleted. A microbial classifier for the prediction of pancreatic ductal adenocarcinoma (PDAC) was developed in the Iranian cohort and evaluated in the Finnish cohort, where it yielded a respectable AUC of 0.88 (95% CI 0.78, 0.97).

CONCLUSIONS

This study highlights the potential of gut microbes as biomarkers for noninvasive PC screening and the development of targeted therapies, emphasizing the need for further research to validate these findings in diverse populations. A comprehensive understanding of the role of the gut microbiome in PC could significantly enhance early detection efforts and improve patient outcomes.

Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial

BACKGROUND

Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

METHODS

We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

RESULTS

With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

CONCLUSIONS

Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

TRIAL REGISTRATION NUMBER

NCT03554083.

Gut microbiota and metabolites are linked to disease progression in multiple sclerosis

Progressive multiple sclerosis (MS) is a neurological disease with limited understanding of the biology associated with transition from relapsing to progressive disease. Intestinal microbes and metabolites are altered in MS, but relation to disease progression is largely unknown. We investigate microbiota and metabolites in subjects with stable MS, those who worsened, and in those with relapsing MS who became progressive over 2 years. We find that Eubacterium hallii, Butyricoccaceae, Blautia, and other short-chain fatty-acid-producing microbes have beneficial associations with worsening of disability, 3T magnetic resonance imaging (MRI) measures, cognition, and quality of life, while Alistipes is detrimentally associated. Global metabolomics identified serum and stool metabolites that are altered in progressive MS and in relapsing subjects who transitioned to progressive disease. Most fecal metabolites associated with disease progression are decreased, suggesting a deficiency of protective factors in the gut. Using a unique MS cohort, our findings identify gut microbiome and metabolite pathways influencing progressive MS.

Microbiome composition and metabolic pathways in shallow and deep periodontal pockets

In periodontal diseases, a dysbiotic subgingival microbiome interacts complexly with the host immune response and is strongly considered a risk factor for various systemic conditions. The high prevalence of both periodontal and systemic diseases in older adults highlights the importance of characterizing the subgingival microbiome in this age group. This study specifically characterizes the composition of the subgingival microbiome and investigates the interactions between microbial niches in shallow and deep periodontal pockets in individuals in their early 70s. We collected 1928 samples from 1287 participants, all born between 1950 and 1951. Participants had either shallow (≤ 4 mm) periodontal pockets or both shallow and deep (≥ 5 mm) periodontal pockets. Distinct microbial patterns were observed in shallow and deep periodontal pockets within the same oral cavity. Deep pockets exhibited a significantly higher abundance of species from genera such as Prevotella, Centipeda, Treponema, and Fusobacterium, while shallow pockets were enriched with species from Actinomyces, Pauljensenia, Streptococcus, and Gemella. The top significant species associated with deep pockets included Fretibacterium fastidiosum, Tannerella forsythia, and Treponema denticola, whereas shallow pockets were predominantly associated with Actinomyces species and Rothia dentocariosa. Additionally, shallow pockets in individuals with both pocket types showed a positive association with Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum compared to shallow pockets in individuals with only shallow pockets. Metabolic pathways showed significant variation with pocket depth, with pathways such as lipopolysaccharide metabolism, lipid metabolism, and polyamine biosynthesis being positively associated with deep pockets. Overall, this study provides comprehensive microbiome analyses of periodontal pockets in aging adults, contributing to a better understanding of periodontal health and its potential impact on reducing systemic health risks in aging populations.

Development of the breastfed infant oral microbiome over the first two years of life in the BLOSOM Cohort

Background

Acquisition and development of the oral microbiome are dynamic processes that occur over early life. This study aimed to characterize the temporal development of the oral microbiome of predominantly breastfed infants during the first two years of life.

Methods

Infant oral samples (n=667) were collected at ten time points from the first week to year two of life from 84 infants. Bacterial DNA profiles were analyzed using full-length 16S rRNA gene sequencing.

Results

The oral microbiome was dominated by Streptococcus mitis, Gemella haemolysans, and Rothia mucilaginosa. Bacterial richness decreased from 1 to 2 months (P = 0.043) and increased from 12 to 24 months (P = 0.038). Shannon diversity increased from 1 week to 1 month and again from 6 to 9 months and 9 to 12 months (all P ≤ 0.04). The composition of the infant oral microbiome was associated with multiple factors, including early pacifier use, intrapartum antibiotic prophylaxis, maternal allergy, pre-pregnancy body mass index, siblings, delivery mode, maternal age, pets at home, and birth season (all P < 0.01). Introduction of solid foods was a significant milestone in oral microbiome development, triggering an increase in bacterial diversity (richness P = 0.0004; Shannon diversity P = 0.0007), a shift in the abundance of seven species, and a change in beta diversity (P = 0.001).

Conclusion

These findings underscore the importance of multiple factors, particularly the introduction of solid foods, in shaping the oral microbiome of breastfed infants during early life.

A multi-omics microbiome signature is associated with the benefits of gastric bypass surgery and is differentiated from diet induced weight loss through 2 years of follow-up

Roux-en-Y gastric bypass (GBP) surgery is an effective treatment for reducing body weight and correcting metabolic dysfunction in individuals with severe obesity. Herein, we characterize the differences between very low energy diet (VLED) and GBP induced weight loss by multi-omic analyses of microbiome and host features in a non-randomized, controlled, single-center study. Eighty-eight participants with severe obesity were recruited into two arms - GBP versus VLED with matching weight loss for 6 weeks and 2-years of follow-up. A dramatic shift in the distribution of gut microbial taxa and their functional capacity was seen in the GBP group at Week 2 after surgery and was sustained through 2 years. Multi-omic analyses were performed after 6 weeks of matching weight loss between the GBP and VLED groups, which pointed to microbiome derived metabolites such as indoxyl sulphate as characterizing the GBP group. We also identified an inverse association between Streptococcus parasanguinis (an oral commensal) and plasma levels of tryptophan and tyrosine. These data have important implications, as they reveal a significant robust restructuring of the microbiome away from a baseline dysbiotic state in the GBP group. Furthermore, multi-omics modelling points to potentially novel mechanistic insights at the intersection of the microbiome and host.

Still not sterile: viability-based assessment of the skin microbiome following pre-surgical application of a broad-spectrum antiseptic reveals transient pathogen enrichment and long-term recovery

Broad-spectrum antiseptics such as chlorhexidine gluconate (CHG) have widespread use as pre-surgical tools to lower skin microbial burden and reduce the risk of surgical site infection. However, the short- and long-term effects of CHG on healthy skin microbial communities remain undefined due to the confounding effects of CHG binding with persistent bacterial DNA on the skin surface. Here, we aim to accurately characterize the immediate and long-term impact of pre-surgical preparation with CHG-based antiseptics on the human skin microbiome. Twenty-eight patients undergoing elective surgeries were enrolled. Swabs of the surgical site and a control site skin microbiome were collected at multiple time points before and up to 2 weeks after surgery. A propidium monoazide (PMAxx)-based viability assay was optimized to selectively evaluate DNA from live microbes in complex skin microbial communities with viability-qPCR and viable 16S ribosomal RNA gene profiling. Pre-operative CHG induces a measurable reduction in the viable microbial bioburden at the surgical site. On the day of surgery, surgical sites displayed a significant increase in the relative abundance of several SSI-associated bacterial genera including Acinetobacter, Bacillus, Escherichia-Shigella, and Pseudomonas compared to baseline. Bacillus species isolated from subjects at baseline also demonstrate resistance to CHG with minimum inhibitory concentrations exceeding 1,000 µg/mL. Although there are major skin microbiome shifts upon exposure to CHG, we also find that these shifts are largely transient. For the majority of individuals, skin microbial bioburden and community structure recover to near baseline by post-surgical follow-up.IMPORTANCESurgical site infections continue to occur despite widespread adoption of surgical antiseptics. Before surgery, patients often wash their whole body multiple times with chlorhexidine gluconate (CHG)-based antiseptic soap and have CHG applied to the surgical site in the operating room. However, the effects of CHG antiseptics on the healthy skin microbiome are undefined due to CHG persisting and binding DNA from dead cells on the skin. We optimized a viability assay to selectively target DNA from live microbes on the skin before and after exposure to CHG. Our findings demonstrate that pre-surgical application of CHG significantly reduces the bioburden on skin; however, potentially pathogenic bacteria remain. Post-surgery, the skin microbiome eventually recovers to resemble its pre-CHG exposed state. Collectively, these findings identify tangible avenues for improving antiseptic formulations and further support that the skin microbiome is viable, stable, and resilient to chemical perturbation.

Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut

Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 107 viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.

House dust microbiome differentiation and phage-mediated antibiotic resistance and virulence dissemination in the presence of endocrine-disrupting chemicals and pharmaceuticals

BACKGROUND

House dust serves as a reservoir of a diverse array of microbial life and anthropogenic chemicals, both of which can potentially influence the health of occupants, particularly those who spend significant amounts of time at home. However, the effects of anthropogenic chemicals on dust microbiomes remain poorly understood. This study investigated the presence of anthropogenic chemicals in the dust of homes occupied by elderly occupants and explored those chemicals' relationships with dust microbiomes.

RESULTS

We detected 69 out of 76 analyzed anthropogenic chemicals, including endocrine-disrupting chemicals, non-antibiotic pharmaceuticals, and antibiotics, in at least one house dust sample from 32 residential homes, with concentrations ranging from 2720 to 89,300 ng/g. Some of these detected compounds were pharmaceuticals regularly consumed by the occupants. The dust microbiomes were associated with varying levels of anthropogenic chemicals, forming two distinct clusters, each with unique diversity, taxonomy, metabolic functions, and resistome profiles. Higher concentrations and a greater variety of these chemicals were associated with an increased co-occurrence of antibiotic resistance and virulence genes, as well as an enhanced potential for their transfer through mobile genetic elements. Under these conditions, phages, especially phage-plasmids, facilitated the dissemination of antibiotic resistance and virulence among bacterial populations.

CONCLUSIONS

The findings indicate that everyday anthropogenic chemicals are important factors associated with the microbes in indoor environments. This underscores the importance of improving household chemical stewardship to reduce the health risks associated with exposure to these chemicals and their effects on indoor microbiomes. Video Abstract.

Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study

AIMS

To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.

METHODS

In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.

RESULTS

The results indicated significant variation in α-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, β-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.

CONCLUSION

These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.

Protocol for microbial profiling of low-biomass upper respiratory tract samples

The upper respiratory tract (URT) microbiota plays a role in both acute and chronic respiratory health outcomes and consists of multiple ecologically distinct niches, all of which have low bacterial biomass. Here, we present a protocol for microbial profiling of low-biomass URT samples. We describe steps for collecting, storing, and extracting DNA. We then detail procedures for performing 16S rRNA sequencing, using an Illumina MiSeq platform, to characterize microbial communities. For complete details on the use and execution of this protocol, please refer to Odendaal et al.1.

Alteration of salivary Streptococcus is associated with statin therapy in older adults: a cohort study

Background

Salivary microbiome alterations are associated with chronic diseases, such as cardiovascular disease, diabetes, and dementia. These chronic diseases often coexist in older adults, leading to polypharmacy. This situation complicates the relationship between systemic diseases and salivary microbiome dysbiosis. Previous studies have demonstrated the association of the human gut microbiome with common prescription drug use, including polypharmacy. However, a comprehensive analysis of the salivary microbiome and prescription drugs is yet to be conducted in older adults. Therefore, in this study, we performed a multivariate analysis to investigate the relationship between salivary microbiomes and host variables, including prescribed drugs, cognitive function, and oral health, in Japanese older adults with different disease backgrounds.

Methods

We enrolled non-hospitalised 82 older adults aged ≥70 years from a Japanese village community, and collected metadata, including age, sex, body mass index, cognitive function, oral health, alcohol consumption, smoking, and common prescription drug information. We performed multivariate analyses and functional predictions on the salivary microbiome based on 16S ribosomal RNA gene amplicon sequencing, including the metadata as potential confounders.

Results

We observed a relationship between the human salivary microbiome and prescribed drug use in Japanese older adults with a heterogeneous background of comorbidities. The effects of several prescribed drugs, such as statins, proton pump inhibitors, and transporter/symporter inhibitors, on the salivary microbiome diversity were more prominent than those of host variables, including age, sex, and oral health. Notably, statin use was strongly correlated with a decrease in the Streptococcus abundance. Furthermore, statin intensity and obesity may be associated with altering the salivary microbiome, including functional predictions for vitamin biosynthesis and purine nucleotide degradation pathways in statin users.

Conclusion

Our multivariate analysis, adjusted for prescribed drug use and non-use, revealed the drug-specific alteration of salivary microbiome composition in Japanese older adults with comorbidities. To our knowledge, this study is the first to described the association of common prescription drug use with salivary microbiome alterations in older adults. Our findings indicated that prescribed drug use is a key factor in understanding the link between salivary microbiome changes and systemic diseases in older adults.

In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier

BACKGROUND

Non-absorbed dietary emulsifiers, including carboxymethylcellulose (CMC), directly disturb intestinal microbiota, thereby promoting chronic intestinal inflammation in mice. A randomised controlled-feeding study (Functional Research on Emulsifiers in Humans, FRESH) found that CMC also detrimentally impacts intestinal microbiota in some, but not all, healthy individuals.

OBJECTIVES

This study aimed to establish an approach for predicting an individual's sensitivity to dietary emulsifiers via their baseline microbiota.

DESIGN

We evaluated the ability of an in vitro microbiota model (MiniBioReactor Arrray, MBRA) to reproduce and predict an individual donor's sensitivity to emulsifiers. Metagenomes were analysed to identify signatures of emulsifier sensitivity.

RESULTS

Exposure of human microbiotas, maintained in the MBRA, to CMC recapitulated the differential CMC sensitivity previously observed in FRESH subjects. Furthermore, select FRESH control subjects (ie, not fed CMC) had microbiotas that were highly perturbed by CMC exposure in the MBRA model. CMC-induced microbiota perturbability was associated with a baseline metagenomic signature, suggesting the possibility of using one's metagenome to predict sensitivity to dietary emulsifiers. Transplant of human microbiotas that the MBRA model deemed CMC-sensitive, but not those deemed insensitive, into IL-10-/- germfree mice resulted in overt colitis following CMC feeding.

CONCLUSION

These results suggest that an individual's sensitivity to emulsifier is a consequence of, and can thus be predicted by, examining their baseline microbiota, paving the way to microbiota-based personalised nutrition.

Associations of prenatal organophosphate esters exposure with risk of eczema in early childhood, mediating role of gut microbiota

Few epidemiological evidence has focused on the impact of organophosphate esters (OPEs) and the risk of eczema, and underlying role of gut microbiota. Based on the Shanghai Maternal-Child Pairs Cohort, a nested case-control study including 332 eczema cases and 332 controls was conducted. Umbilical cord blood and stools were collected for OPEs detection and gut microbiota sequencing, separately. Eczema cases were identified using the International Study of Asthma and Allergies in Childhood core questionnaire and clinical diagnosis. The environmental risk score (ERS) for OPEs was developed to quantify OPEs burden. Conditional logistic regression models, multivariate analysis by linear models, negative-binomial hurdle regression, and mediation analysis were employed. Tris(2-butoxyethyl) phosphate (TBP), tris (2-butoxy ethyl) phosphate (TBEP), 2-ethylhexyl diphenyl phosphate (EHDPP), and tris(1,3-dichloro-2-propyl) phosphate (TDCPP) had detection rates > 50 %, with median concentrations ranged from 0.11 to 2.71 μg/L. TBP (OR = 1.12, 95 % CI: 1.01, 1.25), TDCPP (OR = 1.32, 95 % CI: 1.09, 1.59), and ERS (OR = 6.44, 95 % CI: 3.47, 11.94) were associated with elevated risk of eczema. OPEs exposure was correlated with increased alpha diversity and the abundance of several pathogenic bacteria, such as Klebsiella. Negative associations were observed between OPEs exposure and the abundances of Lachnospiraceae genera. Additionally, a positive correlation was identified between alpha diversity and the risk of eczema during childhood. Alpha diversity indices and Lachnospiraceae serve as significant mediators in this relationship. Results of this study indicate that prenatal exposure to OPEs is linked to an elevated risk of eczema and gut microbiota dysbiosis, potentially contributing to immunotoxicity of OPEs during early life.

Nasal microbiome in relation to olfactory dysfunction and cognitive decline in older adults

Emerging evidence has highlighted that olfactory dysfunction, a common feature of aging, is increasingly linked to cognitive decline in older adults. However, research on the underlying mechanism, particularly the role of nasal microbiome, remains limited. In this study, we investigated the associations between olfactory function, the nasal microbiome, and cognition among 510 older adults with an average age of 77.9 years. Olfactory function was assessed using the brief Chinese Smell Identification Test, and cognitive assessments were conducted via the Mini-Mental State Examination and the Revised Hasegawa Dementia Scale. Nasal microbiome profiles were generated through 16S RNA gene sequencing. We observed that olfactory dysfunction (i.e., hyposmia) was associated with a higher richness of nasal bacteria, and such observation was replicated in an external dataset. A total of 18 nasal bacterial genera were identified to be associated with olfactory function, with eight genera such as Acidovorax and Morganella being enriched in the hyposmic group. A composite microbial index of nasal olfactory function significantly improved the reclassification accuracy of traditional risk model in distinguishing hyposmic from normosmic participants (P = 0.008). Furthermore, participants with a nasal biotype dominated by Corynebacterium had a lower prevalence of mild cognitive impairment compared to those dominated by Dolosigranulum or Moraxella. Our findings suggested that the nasal microbiome may play a role in the association of olfactory function with cognition in older adults, providing new insights into the microbial mechanisms underlying hyposmia and cognitive decline.

Osteoarthritis treatment via the GLP-1-mediated gut-joint axis targets intestinal FXR signaling

Whether a gut-joint axis exists to regulate osteoarthritis is unknown. In two independent cohorts, we identified altered microbial bile acid metabolism with reduced glycoursodeoxycholic acid (GUDCA) in osteoarthritis. Suppressing farnesoid X receptor (FXR)-the receptor of GUDCA-alleviated osteoarthritis through intestine-secreted glucagon-like peptide 1 (GLP-1) in mice. GLP-1 receptor blockade attenuated these effects, whereas GLP-1 receptor activation mitigated osteoarthritis. Osteoarthritis patients exhibited a lower relative abundance of Clostridium bolteae, which promoted the formation of ursodeoxycholic acid (UDCA), a precursor of GUDCA. Treatment with C. bolteae and Food and Drug Administration-approved UDCA alleviated osteoarthritis through the gut FXR-joint GLP-1 axis in mice. UDCA use was associated with lower risk of osteoarthritis-related joint replacement in humans. These findings suggest that orchestrating the gut microbiota-GUDCA-intestinal FXR-GLP-1-joint pathway offers a potential strategy for osteoarthritis treatment.

Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice

BACKGROUND

Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.

RESULTS

Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.

CONCLUSIONS

Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.

Gut microbiome evolution from infancy to 8 years of age

The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.

Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus

Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.

Faecal Cytolysin is Associated With Worse Survival in Patients With Primary Sclerosing Cholangitis

BACKGROUND AND AIMS

Primary sclerosing cholangitis (PSC) is an immune-related cholangiopathy without treatment options beyond liver transplantation. The gut-liver axis, especially the role of gut microbes, has emerged as a crucial pathway contributing to PSC pathogenesis. Recent research has revealed Enterococcus (E.) faecalis and its virulence factor cytolysin to increase mortality risk in patients with alcohol-associated hepatitis. Thus, we studied the role of enterococci, particularly E. faecalis and its virulence factor genes cytolysin and gelatinase, in faecal samples from patients with PSC.

METHODS

To assess the relevance of Enterococcus species, we performed 16S rRNA gene amplicon analysis in faecal samples from 60 patients with PSC. We validated our findings by qPCR of faecal microbial DNA in an extended cohort of 105 patients with PSC, 104 patients with inflammatory bowel disease (IBD) and 68 healthy subjects.

RESULTS

High-throughput 16S rRNA amplicon analysis revealed an increased relative abundance of enterococci in PSC patients compared with healthy controls and IBD patients, respectively, (p < 0.0001). PSC patients with high enterococci abundance had a decreased probability of transplant-free survival (p = 0.028). E. faecalis and its virulence factors cytolysin and gelatinase were more abundant in patients with PSC. Higher faecal cytolysin was associated with lower overall survival (p = 0.04), while survival was independent of gelatinase levels.

CONCLUSION

Our data highlight the association of E. faecalis and faecal cytolysin with lower survival in patients with PSC. These data should prompt further research into the pathogenic role of cytolysin-positive E. faecalis, and to explore its role as a potential therapeutic target.

Gut microbiomes are largely unchanged when exposed to their amphibian host's latitudinally variable upper thermal limit

Climate change will increase the frequency and severity of temperature extremes. Links between host thermal physiology and their gut microbiota suggest that organisms' responses to future climates may be mediated by their microbiomes, raising the question of how the thermal environment influences the microbiome itself. Vertebrate gut microbiomes influence the physiological plasticity of their hosts via effects on immunity, metabolism, and nutrient uptake. The gut microbiota of ectothermic vertebrates in particular are responsive to long-term, sub-lethal gradual increases in environmental temperature. Whether and how the gut microbiota respond to brief exposure to temperatures at the upper limit of host physiological tolerance (CTmax) is poorly understood but could have downstream effects on host fitness. We assayed the CTmax of wood frogs (Lithobates sylvaticus) from 15 populations across a 10° latitudinal gradient. We then characterized the gut microbiota of juveniles at two time points following exposure to CTmax. Frogs from higher latitudes had lower thermal tolerance (lower CTmax) than those from lower latitudes. Unexpectedly, exposure to upper survivable temperature had little to no detectable effect on the frogs' microbiota richness, stability, or composition. Instead, we found a strong effect of time in which frogs kept in recovery conditions for four days had less diverse, but more stable gut microbiota than those that had recovered for only one day, regardless of CTmax exposure. We conclude that while wood frogs from higher latitudes have reduced thermal tolerances than those from lower latitudes, their microbial communities are largely unaffected by brief exposure to high temperatures at the edge of their physiological limits.

Picky eaters: Selective microbial diet of avian ectosymbionts

Individual organisms can function as ecosystems inhabited by symbionts. Symbionts may interact with each other in ways that subsequently influence their hosts positively or negatively, although the details of how these interactions operate collectively are usually not well understood. Vane-dwelling feather mites are common ectosymbionts of birds and are proposed to confer benefits to hosts by consuming feather-degrading microbes. However, it is unknown whether these mites exhibit generalist or selective diets, or how their dietary selection could potentially impact their symbiotic functional nature. In this study, we conducted 16S rDNA and ITS1 amplicon sequencing to examine the microbial diet of feather mites. We characterized and compared the diversity and composition of bacteria and fungi in the bodies of mites living on feathers of the Prothonotary Warbler, Protonotaria citrea, to microbial assemblages present on the same feathers. We found less diverse, more compositionally similar microbial assemblages within mites than on feathers. We also found that mites were resource-selective. Based on the identity and known functions of microbes found within and presumably preferred by mites, our results suggest that these mites selectively consume feather-degrading microbes. Therefore, our results support the proposition that mites confer benefits to their hosts. This study provides insight into symbioses operating at multiple biological levels, highlights the ecological and evolutionary importance of the synergistic interactions between species, and greatly expands our understanding of feather mite biology.