Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

Abstract Background Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome features and their associations with immigration, dietary intake, and obesity in 2640 individuals from a population-based study of US Hispanics/Latinos. Results The fecal shotgun metagenomics data indicate that greater US exposure is associated with reduced ɑ-diversity, reduced functions of fiber degradation, and alterations in individual taxa, potentially related to a westernized diet. However, a majority of gut bacterial genera show paradoxical associations, being reduced with US exposure and increased with fiber intake, but increased with obesity. The observed paradoxical associations are not explained by host characteristics or variation in bacterial species but might be related to potential microbial co-occurrence, as seen by positive correlations among Roseburia, Prevotella, Dorea, and Coprococcus. In the conditional analysis with mutual adjustment, including all genera associated with both obesity and US exposure in the same model, the positive associations of Roseburia and Prevotella with obesity did not persist, suggesting that their positive associations with obesity might be due to their co-occurrence and correlations with obesity-related taxa, such as Dorea and Coprococcus. Conclusions Among US Hispanics/Latinos, US exposure is associated with unfavorable gut microbiome profiles for obesity risk, potentially related to westernized diet during acculturation. Microbial co-occurrence could be an important factor to consider in future studies relating individual gut microbiome taxa to environmental factors and host health and disease.

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Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa022 ◽

2020 ◽

Vol 96 (3) ◽

Cited By ~ 2

Author(s):

Gavin J Fenske ◽

Sudeep Ghimire ◽

Linto Antony ◽

Jane Christopher-Hennings ◽

Joy Scaria

Keyword(s):

Bacterial Communities ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Culture Techniques ◽

Microbiome Composition ◽

Culture Independent ◽

Health And Disease ◽

The Media ◽

And Function ◽

Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

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Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats

10.1101/2021.05.06.442639 ◽

2021 ◽

Author(s):

Silvia Raineri ◽

Julia A Sherriff ◽

Kevin S.J Thompson ◽

Huw Jones ◽

Paul T Pfluger ◽

...

Keyword(s):

Weight Loss ◽

Food Intake ◽

Detailed Analysis ◽

Relative Abundance ◽

Gut Microbiome ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Fecal Microbiome ◽

Obese Rats ◽

The Impact

Background: Obesity, metabolic disease and some psychiatric conditions are associated with changes to relative abundance of bacterial species and specific genes in the fecal microbiome. Little is known about the impact of pharmacologically induced weight loss on distinct gut microbiome species and their respective gene programs in obese individuals. Results: Using shotgun metagenomics, the composition of the microbiome was obtained for two cohorts of obese female Wistar rats (n=10-12, total of 82) maintained on a high fat diet before and after a 42-day treatment with a panel of four anti-obesity drugs (tacrolimus/FK506, bupropion, naltrexone and sibutramine), alone or in combination. We found that sibutramine treatment induced consistent weight loss through reducing food intake. Decreased weight loss in sibutramine-treated rats was associated with changes to the gut microbiome that included increased beta-diversity, increased Bacteroides/Firmicutes ratio and increased relative abundance of multiple Bacteroides species. In addition, the relative abundance of multiple genes was found to be differentially abundant, including significant reductions in components of flagellum and genes involved in flagellum assembly. Conclusions: This study provides a large resource comprising complete shotgun metagenomics datasets of the fecal microbiome coupled with weight change and food intake at day 3, day 15 and day 42 from 82 obese rats treated with a range of compounds used for weight loss, which are available to the community for detailed analysis. Furthermore, by conducting a detailed analysis of the microbiome associated with sibutramine-induced weight loss, we have identified multiple weight-loss associated microbial taxa and pathways. These include a reduction in components of flagellum and the flagellum assembly pathway that points to a potential role of sibutramine-induced weight-loss on regulating bacterially driven anti-inflammatory responses.

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Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy and the host’s genotype upon microbiome composition

10.1101/571430 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jian Yin ◽

Peter R. Sternes ◽

Mingbang Wang ◽

Mark Morrison ◽

Jing Song ◽

...

Keyword(s):

Ankylosing Spondylitis ◽

Gut Microbiome ◽

Bacterial Species ◽

Tnf Inhibitor ◽

Hla B27 ◽

Clinical Genetic ◽

Host Genotype ◽

Shotgun Metagenomics ◽

Microbiome Composition ◽

Immune Mediated

ABSTRACTDiverse evidence including clinical, genetic and microbiome studies support a major role of the gut microbiome in the common immune-mediated arthropathy, ankylosing spondylitis (AS). To further investigate this we performed metagenomic analysis of a case-control cohort of 250 Han-Chinese subjects. Previous reports of gut dysbiosis in AS were re-confirmed and several notable bacterial species and functional categories were differentially abundant. TNF-inhibitor (TNFi) therapy at least partially restored the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. Enrichment of bacterial peptides homologous to HLA-B27-presented epitopes was observed in the stools of AS patients, suggesting that either HLA-B27 fails to clear these or that they are involved in driving HLA-B27-associated immune reactions. TNFi therapy of AS patients was also associated with a reduction of potentially arthritogenic bacterial peptides, relative to untreated patients. An AS-associated SNP in RUNX3 significantly influenced the microbiome in two independent cohorts, highlighting a host genotype (other than HLA-B27) potentially influencing AS via the microbiome. These findings emphasise the key role that the gut microbiome plays in driving the pathogenesis of AS.

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Microbial Signature of Ocean-Going Syndrome

10.21203/rs.3.rs-66121/v1 ◽

2020 ◽

Author(s):

Zheng Sun ◽

Meng Zhang ◽

Min Li ◽

Jinshan Zhao ◽

Youran Ji ◽

...

Keyword(s):

Health Status ◽

Gut Microbiome ◽

Bacterial Species ◽

Extreme Environments ◽

Gene Families ◽

Working Environment ◽

Shotgun Metagenomics ◽

Before And After ◽

Key Factor ◽

Optimal Health

Abstract Background and aims: During ocean-going voyages, crew members are subject to complex pressures from their living and working environment, which leads to a sub-optimal health status. Although abnormal defecation was observed during voyages, the associations between the gut microbiome and the symptoms are still unclear. Methods: Associations between the gut microbiome and the health status of 77 crew members during a 135 day-long ocean-going voyage were evaluated using shotgun metagenomics of stool samples and health questionnaires (with 24 physical and psychological indicators) taken before and after the voyage.Results: The co-appearance of symptoms e.g. abnormal defecation frequency, insomnia, shallow sleep, nausea and over-eating best described the sub-optimal health status of the majority of crew members, and we named this as ‘Ocean-Going Syndrome (OGS)’. The OGS, instead of any single symptom, has a significant effect on the gut microbiome, and it was proved to be a key factor for individual perturbation in the gut microbiome during the voyage. Co-occurrence network analysis revealed a different microbial dynamic between the OGS and non-OGS crews, and the variation of 19 bacterial species and 31 gene families were identified as microbial signature for the OGS. Moreover, using a Random Forest model, the OGS can be predicted with a high accuracy (AUC=0.91) based on 27 biomarkers from pre-voyage samples. Conclusions: Understanding associations between the gut microbiome and health status under extreme environments could help us discover potential predictors or even therapeutic targets for dysbacteriosis related diseases.

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Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk

Circulation Research ◽

10.1161/circresaha.118.314642 ◽

2019 ◽

Vol 124 (12) ◽

pp. 1808-1820 ◽

Cited By ~ 33

Author(s):

Alexander Kurilshikov ◽

Inge C.L. van den Munckhof ◽

Lianmin Chen ◽

Marc J. Bonder ◽

Kiki Schraa ◽

...

Keyword(s):

Gut Microbiome ◽

Bacterial Species ◽

Short Chain Fatty Acids ◽

Population Based ◽

Liver Fat ◽

Plasma Metabolites ◽

Cvd Risk ◽

Microbial Composition ◽

Lipoprotein Subclasses ◽

Microbial Associations

Rationale: Altered gut microbial composition has been linked to cardiovascular diseases (CVDs), but its functional links to host metabolism and immunity in relation to CVD development remain unclear. Objectives: To systematically assess functional links between the microbiome and the plasma metabolome, cardiometabolic phenotypes, and CVD risk and to identify diet-microbe-metabolism-immune interactions in well-documented cohorts. Methods and Results: We assessed metagenomics-based microbial associations between 231 plasma metabolites and microbial species and pathways in the population-based LLD (Lifelines DEEP) cohort (n=978) and a clinical obesity cohort (n=297). After correcting for age, sex, and body mass index, the gut microbiome could explain ≤11.1% and 16.4% of the variation in plasma metabolites in the population-based and obesity cohorts, respectively. Obese-specific microbial associations were found for lipid compositions in the VLDL, IDL, and LDL lipoprotein subclasses. Bacterial L-methionine biosynthesis and a Ruminococcus species were associated to cardiovascular phenotypes in obese individuals, namely atherosclerosis and liver fat content, respectively. Integration of microbiome-diet-inflammation analysis in relation to metabolic risk score of CVD in the population cohort revealed 48 microbial pathways associated to CVD risk that were largely independent of diet and inflammation. Our data also showed that plasma levels rather than fecal levels of short-chain fatty acids were relevant to inflammation and CVD risk. Conclusions: This study presents the largest metagenome-based association study on plasma metabolism and microbiome relevance to diet, inflammation, CVD risk, and cardiometabolic phenotypes in both population-based and clinical obesity cohorts. Our findings identified novel bacterial species and pathways that associated to specific lipoprotein subclasses and revealed functional links between the gut microbiome and host health that provide a basis for developing microbiome-targeted therapy for disease prevention and treatment.

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Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2019-215763 ◽

2019 ◽

Vol 79 (1) ◽

pp. 132-140 ◽

Cited By ~ 16

Author(s):

Jian Yin ◽

Peter Richard Sternes ◽

Mingbang Wang ◽

Jing Song ◽

Mark Morrison ◽

...

Keyword(s):

Ankylosing Spondylitis ◽

Gut Microbiome ◽

Bacterial Species ◽

Metagenomic Sequencing ◽

Healthy Controls ◽

Hla B27 ◽

Clinical Genetic ◽

Shotgun Metagenomics ◽

Microbiome Composition ◽

Shotgun Metagenomic Sequencing

ObjectivesDiverse evidence including clinical, genetic and microbiome studies support a major role of the gut microbiome in the common immune-mediated arthropathy, ankylosing spondylitis (AS). We set out to (1) further define the key microbial characteristics driving disease, and (2) examine the effects of tumour necrosis factor-inhibitor (TNFi) therapy upon the microbiome.MethodsThe stools from a case–control cohort of 250 Han-Chinese subjects underwent shotgun metagenomic sequencing. All subjects were genotyped using the Illumina CoreExome SNP microarray.ResultsPrevious reports of gut dysbiosis in AS were reconfirmed and several notable bacterial species and functional categories were differentially abundant. TNFi therapy was correlated with a restoration the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. Enrichment of bacterial peptides homologous to HLA-B27-presented epitopes was observed in the stools of patients with AS, suggesting that either HLA-B27 fails to clear these or that they are involved in driving HLA-B27-associated immune reactions. TNFi therapy largely restored the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. TNFi therapy of patients with AS was also associated with a reduction of potentially arthritogenic bacterial peptides, relative to untreated patients.ConclusionThese findings emphasise the key role that the gut microbiome plays in driving the pathogenesis of AS and highlight potential therapeutic and/or preventative targets.

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Pharmacologically Induced Weight Loss Is Associated With Distinct Gut Microbiome Changes In Obese Rats

10.21203/rs.3.rs-544257/v2 ◽

2021 ◽

Author(s):

Silvia Raineri ◽

Julia A Sherriff ◽

Kevin S.J. Thompson ◽

Huw Jones ◽

Paul T Pfluger ◽

...

Keyword(s):

Weight Loss ◽

Food Intake ◽

Detailed Analysis ◽

Relative Abundance ◽

Gut Microbiome ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Fecal Microbiome ◽

Obese Rats ◽

The Impact

Abstract Background: Obesity, metabolic disease and some psychiatric conditions are associated with changes to relative abundance of bacterial species and specific genes in the fecal microbiome. Little is known about the impact of pharmacologically induced weight loss on distinct gut microbiome species and their respective gene programs in obese individuals. Results: Using shotgun metagenomics, the composition of the microbiome was obtained for two cohorts of obese female Wistar rats (n=10-12, total of 82) maintained on a high fat diet before and after a 42-day treatment with a panel of four investigatory or approved anti-obesity drugs (tacrolimus/FK506, bupropion, naltrexone and sibutramine), alone or in combination. We found that sibutramine treatment induced consistent weight loss through reducing food intake. Weight loss in sibutramine-treated rats was associated with changes to the gut microbiome that included increased beta-diversity, increased Bacteroides/Firmicutes ratio and increased relative abundance of multiple Bacteroides species. In addition, the relative abundance of multiple genes was found to be differentially abundant, including significant reductions in components of flagellum and genes involved in flagellum assembly. Conclusions: This study provides a large resource comprising complete shotgun metagenomics datasets of the fecal microbiome coupled with weight change and food intake at day 3, day 15 and day 42 from 82 obese rats treated with a range of compounds used for weight loss, which are available to the community for detailed analysis. Furthermore, by conducting a detailed analysis of the microbiome associated with sibutramine-induced weight loss, we have identified multiple weight-loss associated microbial taxa and pathways. These include a reduction in components of flagellum and the flagellum assembly pathway that points to a potential role of sibutramine-induced weight-loss on regulating bacterially driven anti-inflammatory responses.

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Pharmacologically induced weight loss is associated with distinct gut microbiome changes in obese rats

10.21203/rs.3.rs-544257/v1 ◽

2021 ◽

Author(s):

Silvia Raineri ◽

Julia A Sherriff ◽

Kevin S.J. Thompson ◽

Huw Jones ◽

Paul T Pfluger ◽

...

Keyword(s):

Weight Loss ◽

Food Intake ◽

Detailed Analysis ◽

Relative Abundance ◽

Gut Microbiome ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Fecal Microbiome ◽

Obese Rats ◽

The Impact

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Xenobiotics and the Gut Microbiome in Health and Disease

10.3389/978-2-88963-082-0 ◽

2019 ◽

Keyword(s):

Gut Microbiome ◽

Health And Disease

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Nutritional Components in Western Diet Versus Mediterranean Diet at the Gut Microbiota–Immune System Interplay. Implications for Health and Disease

Nutrients ◽

10.3390/nu13020699 ◽

2021 ◽

Vol 13 (2) ◽

pp. 699

Author(s):

Cielo García-Montero ◽

Oscar Fraile-Martínez ◽

Ana M. Gómez-Lahoz ◽

Leonel Pekarek ◽

Alejandro J. Castellanos ◽

...

Keyword(s):

Immune System ◽

Gut Microbiota ◽

Mediterranean Diet ◽

Inflammatory Disorder ◽

Immune Functions ◽

Treatment And Prevention ◽

Nutritional Components ◽

Westernized Diet ◽

Prevention And Health Promotion ◽

Health And Disease

The most prevalent diseases of our time, non-communicable diseases (NCDs) (including obesity, type 2 diabetes, cardiovascular diseases and some types of cancer) are rising worldwide. All of them share the condition of an “inflammatory disorder”, with impaired immune functions frequently caused or accompanied by alterations in gut microbiota. These multifactorial maladies also have in common malnutrition related to physiopathology. In this context, diet is the greatest modulator of immune system–microbiota crosstalk, and much interest, and new challenges, are arising in the area of precision nutrition as a way towards treatment and prevention. It is a fact that the westernized diet (WD) is partly responsible for the increased prevalence of NCDs, negatively affecting both gut microbiota and the immune system. Conversely, other nutritional approaches, such as Mediterranean diet (MD), positively influence immune system and gut microbiota, and is proposed not only as a potential tool in the clinical management of different disease conditions, but also for prevention and health promotion globally. Thus, the purpose of this review is to determine the regulatory role of nutritional components of WD and MD in the gut microbiota and immune system interplay, in order to understand, and create awareness of, the influence of diet over both key components.

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