Gut Microbiome In Response Research Articles

Highly multiplexed spatial mapping of microbial communities.

Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density1 and rich diversity2 of species in environmental microbiomes and the limitations of optical imaging technology3–6. Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence in situ Hybridization (HiPR-FISH), a versatile technology that uses binary encoding, spectral imaging, and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli isolates, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and single-cell image analysis, reveals the disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment and the longitudinal stability of spatial architectures in the human oral plaque microbiome. Combined with super-resolution imaging, HiPR-FISH reveals the diverse ribosome organization strategies of human oral microbial taxa. HiPR-FISH provides a framework for analyzing the spatial ecology of environmental microbial communities at single-cell resolution.

Sex-Specific Differences in the Gut Microbiome in Response to Dietary Fiber Supplementation in IL-10-Deficient Mice.

There is growing interest in studying dietary fiber to stimulate microbiome changes that might prevent or alleviate inflammatory bowel disease (IBD). However, dietary fiber effects have shown varying degrees of efficacy, for reasons that are unclear. This study examined whether the effects of isomaltodextrin on gut microbiota and IBD were dependent on dose or host sex, using an Interleukin (IL)-10 deficient murine colitis model. After 12 weeks, colonic IL-12p70 was depressed in male mice receiving high-dose isomaltodextrin supplementation compared to the control group (p = 0.04). Male mice receiving high-dose isomaltodextrin exhibited changes in microbial alpha-diversity, including enhanced richness and evenness (p = 0.01) and limited reduction in the relative abundance of Coprococcus (q = 0.08), compared to the control group. These microbial compositional changes were negatively associated with IL-12p70 levels in the male group (rs ≤ −0.51, q ≤ 0.08). In contrast, female mice receiving isomaltodextrin displayed a reduction in alpha-diversity and Coprococcus abundance and a high level of IL-12p70, as did the control group. Together, these results indicate that isomaltodextrin altered the gut microbial composition linking specific immune-regulatory cytokine responses, while the interactions among fiber, microbiota and immune response were dose dependent and largely sex specific. The results further indicate that interactions between environmental and host factors can affect microbiome manipulation in the host.

Rotavirus infection induces glycan availability to promote ileum-specific changes in the microbiome aiding rotavirus virulence

ABSTRACT Multiple studies have identified changes within the gut microbiome in response to diarrheal-inducing bacterial pathogens. However, examination of the microbiome in response to viral pathogens remains understudied. Compounding this, many studies use fecal samples to assess microbiome composition; which may not accurately mirror changes within the small intestine, the primary site for most enteric virus infections. As a result, the functional significance of small intestinal microbiome shifts during infection is not well defined. To address these gaps, rotavirus-infected neonatal mice were examined for changes in bacterial community dynamics, host gene expression, and tissue recovery during infection. Profiling bacterial communities using 16S rRNA sequencing suggested significant and distinct changes in ileal communities in response to rotavirus infection, with no significant changes for other gastrointestinal (GI) compartments. At 1-d post-infection, we observed a loss in Lactobacillus species from the ileum, but an increase in Bacteroides and Akkermansia, both of which exhibit mucin-digesting capabilities. Concomitant with the bacterial community shifts, we observed a loss of mucin-filled goblet cells in the small intestine at d 1, with recovery occurring by d 3. Rotavirus infection of mucin-producing cell lines and human intestinal enteroids (HIEs) stimulated release of stored mucin granules, similar to in vivo findings. In vitro, incubation of mucins with Bacteroides or Akkermansia members resulted in significant glycan degradation, which altered the binding capacity of rotavirus in silico and in vitro. Taken together, these data suggest that the response to and recovery from rotavirus-diarrhea is unique between sub-compartments of the GI tract and may be influenced by mucin-degrading microbes.

Metabolically similar cohorts of bacteria exhibit strong cooccurrence patterns with diet items and eukaryotic microbes in lizard guts.

Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist‐insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacterial species that are highly similar to each other metabolically. This pattern in the bacterial microbiome could represent an early step in the taxonomic shifts in bacterial microbiome that occur when host lineages change their diet niche over evolutionary timescales.

Looking like the locals - gut microbiome changes post-release in an endangered species

BackgroundCaptivity presents extreme lifestyle changes relative to the wild, and evidence of microbiome dysbiosis in captive animals is growing. The gut microbiome plays a crucial role in host health. Whilst captive breeding and subsequent reintroduction to the wild is important for conservation, such efforts often have limited success. Post-release monitoring is essential for assessing translocation success, but changes to the microbiome of released individuals are poorly understood. The Tasmanian devil was previously shown to exhibit loss of microbiome diversity as a result of intense captive management. This current study examines changes in the devil gut microbiome in response to translocation and aims to determine if perturbations from captivity are permanent or reversible.MethodsUsing 16S rRNA amplicon sequencing, we conducted temporal monitoring of the gut microbiome of released devils during two translocation events, captive-to-wild and wild-to-wild. To investigate whether the microbiome of the released devils changed following translocation, we characterized their microbiome at multiple time points during the translocation process over the course of 6–12 months and compared them to the microbiome of wild incumbent devils (resident wild-born devils at the respective release sites).ResultsWe showed that the pre-release microbiome was significantly different to the microbiome of wild incumbent animals, but that the microbiomes of animals post-release (as early as 3 to 4 weeks post-release) were similar to wild incumbents. The gut microbiome of released animals showed significant compositional shifts toward the wild incumbent microbiome of both translocation events.ConclusionOur results suggest that the devil gut microbiome is dynamic and that loss of microbiome diversity in captivity can be restored following release to the wild. We recommend the broader application of microbiome monitoring in wildlife translocation programs to assess the impacts of translocation on animal microbiomes.

Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment.

Immunotherapy could change the complex host-microbial interactions. We aimed to investigate the dynamics of gut microbiome in response to secukinumab [an interleukin (IL)-17 inhibitor] and ustekinumab (an IL-12/23 inhibitor) therapy and its association with treatment response in psoriasis. This observational, longitudinal study collected a total of 114 fecal samples from 12 healthy controls and 34 patients with psoriasis at baseline and 3 and 6months after secukinumab (n = 24) or ustekinumab treatment (n = 10) and gut microbiomes were investigated using next-generation sequencing targeting 16S ribosomal RNA. Secukinumab treatment causes more profound alterations in gut microbiome, including increases in the relative abundance of phylum Proteobacteria and decreases in Bacteroidetes and Firmicutes, than ustekinumab treatment. The relative abundance of family Pseudomonadaceae, family Enterobacteriaceae and order Pseudomonadales also increased significantly following secukinumab therapy. In contrast, there was no significant change in gut microbiome composition following ustekinumab treatment, and only genus Coprococcus significantly increased after 6months of ustekinumab therapy. Moreover, we observed significant differences in baseline gut microbiome between responders and non-responders to secukinumab treatment. These results indicate that gut microbiome is altered differently after anti-IL17 and anti-IL12/23 treatment. Secukinumab (anti-IL17) therapy is associated with distinct and more profound gut microbiome shifts than ustekinumab therapy (anti-IL 12/23) in patients with psoriasis. Moreover, gut microbiome would serve as potential biomarkers of response to secukinumab treatment.

Abstract 2838: The gut microbiome (GM) and immunotherapy response are influenced by host lifestyle factors

Abstract Background: There is a growing appreciation for the GM in response to melanoma therapy. Recent work identified a favorable (T1) GM signature associated with checkpoint benefit. However, little is known about how lifestyle factors may influence features of the GM or about the influence of the GM on therapeutic outcomes to other common melanoma therapies. Methods: We prospectively collected fecal samples melanoma patients at MD Anderson Cancer Center and characterized the GM via 16S rRNA sequencing (n=146). In a subset initiating systemic therapy (n= 113), we also collected baseline diet information via the NCI dietary screener questionnaire, and probiotic and antibiotic use and followed for response (RECISTv1.1). We compared GM beta diversity (BD)(Bray-Curtis) with ANOSIM and descriptive statistics and Wilcoxon tests were applied to alpha diversity (AD)(Chao1) among treatment response groups. Spearman correlation was used to test relationships of dietary groups and GM composition. Univariate and multivariate logistic regression models were used to determine the individual and joint effects of lifestyle factors on response. Receiver operating characteristic (ROC) curves were constructed for area under the curve (AUC) quantification. Results: Considering all treatment groups, baseline AD was highest in patients with complete/partial response (mean=355), compared to patients with stable (mean=330) and progressive disease (mean=318). The GM did not significantly differ by age, sex or BMI. Report of probiotic (42%) and antibiotic (29%) use at baseline was associated with lower AD (p=0.02). Whole grains and overall diet quality correlated positively with pro-response bacteria, added sugars and processed meat negatively correlated. GM community structure (BD) differed by high and low fiber intake (p<0.05). Patients with high vs. low fiber diet had higher odds of response to aPD1 (OR=5.3, 95% CI: 1.02-26.3) and AUC for fiber in predicting response was 0.65. Joint effects analysis showed greatest odds of response among patients with a T1 signature and high fiber diet (OR=3.6, 95% CI: 0.7-17.8) vs. low fiber diet (OR=1.9, 95%CI 0.6-6.4), compared to patients without a T1 signature. Similar results were seen for overall diet score; and for both fiber and diet score, results reached statistical significance excluding patients on antibiotics. Conclusion: AD of the GM varies by response regardless of treatment type. While preliminary, this data points to the idea that the GM in melanoma patients may be negatively influenced by probiotics and could be targeted by dietary manipulation. Larger prospective and interventional studies are needed to assess the relationships between host lifestyle factors, the GM and response to melanoma therapies. Citation Format: Christine N. Spencer, Vancheswaran Gopalakrishnan, Jennifer McQuade, Miles C. Andrews, Beth Helmink, M.A. Wadud Khan, Elizabeth Sirmans, Lauren Haydu, Alexandria Cogdill, Elizabeth Burton, Rodabe Amaria, Sapna Patel, Isabella Glitza, MIchael Davies, Eliza Posada, Wen-Jen Hwu, Adi Diab, Kelly Nelson, Hussein Tawbi, Michael Wong, Robert R. Jenq, Lorenzo Cohen, Carrie Daniel-MacDougall, Jennifer A. Wargo. The gut microbiome (GM) and immunotherapy response are influenced by host lifestyle factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2838.

Four men in a boat: Ultra-endurance exercise alters the gut microbiome

ObjectivesCompositional and functional adaptions occur in the gut microbiome in response to habitual physical activity. The response of the gut microbiome to sustained, intense exercise in previously active individuals, however, is unknown. This study aimed to prospectively explore the gut microbiome response of four well-trained male athletes to prolonged, high intensity trans-oceanic rowing, describing changes in microbial diversity, abundance and metabolic capacity. DesignA prospective, repeated-measures, within-subject report. MethodsSerial stool samples were obtained from four male athletes for metagenomic whole-genome shotgun sequencing to record microbial community structure and relevant functional gene profiles before, during and after a continuous, unsupported 33-day, 5000 km transoceanic rowing race. Calorific intake and macronutrient composition were recorded by validated food frequency questionnaire and anthropometry was determined by body composition analysis and cardiorespiratory testing. ResultsMicrobial diversity increased throughout the ultra-endurance event. Variations in taxonomic composition included increased abundance of butyrate producing species and species associated with improved metabolic health, including improved insulin sensitivity. The functional potential of bacterial species involved in specific amino and fatty acid biosynthesis also increased. Many of the adaptions in microbial community structure and metaproteomics persisted at three months follow up. ConclusionsThese findings demonstrate that prolonged, intense exercise positively influences gut microbial diversity, increases the relative abundance of some bacterial species and up-regulates the metabolic potential of specific pathways expressing microbial gene products. These adaptions may play a compensatory role in controlling the physiological stress associated with sustained exertion as well as negating the deleterious consequences accompanying endurance exercise.

Seasonal Variation in Human Gut Microbiome Composition

The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet.