Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM

Abstract Background Men who have sex with men (MSM) have been disproportionately affected by HIV-1 since the beginning of the AIDS pandemic, particularly in the USA and Europe. Compared to men who have sex with women (MSW), MSM have a distinct fecal microbiome regardless of HIV-1 infection. However, it is unclear whether the MSM-associated gut microbiome affects the susceptibility and progression of HIV-1 infection. We studied fecal microbiome profiles, short-chain fatty acids, and blood plasma inflammatory cytokines of 109 HIV-1 seroconverters (SC) from the early, 1984–1985 phase of the HIV-1 pandemic in the Multicenter AIDS Cohort Study (MACS) before and after HIV-1 infection compared to 156 HIV-1-negative MACS MSM (negative controls [NC]). Results We found that family Succinivibrionaceae, S24-7, Mogibacteriaceae, Coriobacteriaceae, and Erysipelotrichaceae were significantly higher (p<0.05), whereas Odoribacteraceae, Verucomicrobiaceae, Bacteroidaceae, Barnesiellaceae, and Rikenellaceae were significantly lower (p<0.05), in SC before HIV-1 infection compared to NC. At the species level, Prevotella stercorea, Eubacterium biforme, and Collinsella aerofaciens were significantly higher (p<0.05), and Eubacterium dolichum, Desulfovibrio D168, Alistipes onderdonkii, Ruminococcus torques, Bacteroides fragilis, Bacteroides caccae, Alistipes putredinis, Akkermansia muciniphila, Bacteroides uniformis, and Bacteroides ovatus were significantly lower (p<0.05) in SC before HIV-1 infection compared to NC. After HIV-1 infection, family Prevotellaceae and Victivallaceae and species Bacteroides fragilis and Eubacterium cylindroides were significantly higher (p<0.05) in SC who developed AIDS within 5 years compared to the SC who were AIDS free for more than 10 years without antiretroviral therapy (ART). In addition, family Victivallaceae and species Prevotella stercorea, Coprococcus eutactus, and Butyrivibrio crossotus were significantly higher (p<0.05) and Gemmiger formicilis and Blautia obeum were significantly lower (p<0.05) after HIV-1 infection in SC who developed AIDS within 5–10 years compared to the SC who were AIDS-free for more than 10 years without ART. Furthermore, plasma inflammatory cytokine levels of sCD14, sCD163, interleukin 6, and lipopolysaccharide binding protein were significantly higher in SC with p<0.05 before HIV-1 infection compared to NC. Conclusions Our results suggest that pathogenic changes in the gut microbiome were present in MSM several months prior to infection with HIV-1 in the early phase of the AIDS pandemic in the USA. This was associated with increased inflammatory biomarkers in the blood and risk for development of AIDS.

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Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases Bacteroides fragilis Abundance Compared with an Isocaloric Snack in College Freshmen

Current Developments in Nutrition ◽

10.1093/cdn/nzz079 ◽

2019 ◽

Vol 3 (8) ◽

Cited By ~ 7

Author(s):

Jaapna Dhillon ◽

Zhaoping Li ◽

Rudy M Ortiz

Keyword(s):

Gut Microbiome ◽

College Freshmen ◽

Bacteroides Fragilis ◽

Alpha Diversity ◽

Control Group ◽

Dietary Regimen ◽

Unifrac Distance ◽

Fecal Microbiome ◽

Microbiome Diversity ◽

Cardiometabolic Disorders

ABSTRACT Background Changes in gut microbiota are associated with cardiometabolic disorders and are influenced by diet. Almonds are a rich source of fiber, unsaturated fats, and polyphenols, all nutrients that can favorably alter the gut microbiome. Objectives The aim of this study was to examine the effects of 8 wk of almond snacking on the gut (fecal) microbiome diversity and abundance compared with an isocaloric snack of graham crackers in college freshmen. Methods A randomized, controlled, parallel-arm, 8-wk intervention in 73 college freshmen (age: 18–19 y; 41 women and 32 men; BMI: 18–41 kg/m2) with no cardiometabolic disorders was conducted. Participants were randomly allocated to either an almond snack group (56.7 g/d; 364 kcal; n = 38) or graham cracker control group (77.5 g/d; 338 kcal/d; n = 35). Stool samples were collected at baseline and 8 wk after the intervention to assess primary microbiome outcomes, that is, gut microbiome diversity and abundance. Results Almond snacking resulted in 3% greater quantitative alpha-diversity (Shannon index) and 8% greater qualitative alpha-diversity (Chao1 index) than the cracker group after the intervention (P < 0.05). Moreover, almond snacking for 8 wk decreased the abundance of the pathogenic bacterium Bacteroides fragilis by 48% (overall relative abundance, P < 0.05). Permutational multivariate ANOVA showed significant time effects for the unweighted UniFrac distance and Bray–Curtis beta-diversity methods (P < 0.05; R2 ≤ 3.1%). The dietary and clinical variables that best correlated with the underlying bacterial community structure at week 8 of the intervention included dietary carbohydrate (percentage energy), dietary fiber (g), and fasting total and HDL cholesterol (model Spearman rho = 0.16; P = 0.01). Conclusions Almond snacking for 8 wk improved alpha-diversity compared with cracker snacking. Incorporating a morning snack in the dietary regimen of predominantly breakfast-skipping college freshmen improved the diversity and composition of the gut microbiome. This trial was registered at clinicaltrials.gov as NCT03084003.

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Usefulness of Machine Learning-Based Gut Microbiome Analysis for Identifying Patients with Irritable Bowels Syndrome

Journal of Clinical Medicine ◽

10.3390/jcm9082403 ◽

2020 ◽

Vol 9 (8) ◽

pp. 2403

Author(s):

Hirokazu Fukui ◽

Akifumi Nishida ◽

Satoshi Matsuda ◽

Fumitaka Kira ◽

Satoshi Watanabe ◽

...

Keyword(s):

Machine Learning ◽

Prediction Model ◽

Gut Microbiome ◽

Clinical Symptoms ◽

Short Chain Fatty Acids ◽

Gas Chromatography Mass Spectrometry ◽

Healthy Controls ◽

Fecal Microbiome ◽

Microbiome Analysis ◽

Model Based

Irritable bowel syndrome (IBS) is diagnosed by subjective clinical symptoms. We aimed to establish an objective IBS prediction model based on gut microbiome analyses employing machine learning. We collected fecal samples and clinical data from 85 adult patients who met the Rome III criteria for IBS, as well as from 26 healthy controls. The fecal gut microbiome profiles were analyzed by 16S ribosomal RNA sequencing, and the determination of short-chain fatty acids was performed by gas chromatography–mass spectrometry. The IBS prediction model based on gut microbiome data after machine learning was validated for its consistency for clinical diagnosis. The fecal microbiome alpha-diversity indices were significantly smaller in the IBS group than in the healthy controls. The amount of propionic acid and the difference between butyric acid and valerate were significantly higher in the IBS group than in the healthy controls (p < 0.05). Using LASSO logistic regression, we extracted a featured group of bacteria to distinguish IBS patients from healthy controls. Using the data for these featured bacteria, we established a prediction model for identifying IBS patients by machine learning (sensitivity >80%; specificity >90%). Gut microbiome analysis using machine learning is useful for identifying patients with IBS.

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Dysbiotic Fecal Microbiome in HIV-1 Infected Individuals in Ghana

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.646467 ◽

2021 ◽

Vol 11 ◽

Author(s):

Prince Kofi Parbie ◽

Taketoshi Mizutani ◽

Aya Ishizaka ◽

Ai Kawana-Tachikawa ◽

Lucky Ronald Runtuwene ◽

...

Keyword(s):

Metabolic Disorders ◽

Alpha Diversity ◽

West African ◽

Cross Sectional ◽

Fecal Microbiome ◽

African Populations ◽

And Gender ◽

Sex With Men ◽

Hiv 1 ◽

Control Study

HIV-1 infected individuals under antiretroviral therapy can control viremia but often develop non-AIDS diseases such as cardiovascular and metabolic disorders. Gut microbiome dysbiosis has been indicated to be associated with progression of these diseases. Analyses of gut/fecal microbiome in individual regions are important for our understanding of pathogenesis in HIV-1 infections. However, data on gut/fecal microbiome has not yet been accumulated in West Africa. In the present study, we examined fecal microbiome compositions in HIV-1 infected adults in Ghana, where approximately two-thirds of infected adults are females. In a cross-sectional case-control study, age- and gender-matched HIV-1 infected adults (HIV+; n = 55) and seronegative controls (HIV-; n = 55) were enrolled. Alpha diversity of fecal microbiome in HIV+ was significantly reduced compared to HIV- and associated with CD4 counts. HIV+ showed reduction in varieties of bacteria including Faecalibacterium, the most abundant in seronegative controls, but enrichment of Proteobacteria. Ghanaian HIV+ exhibited enrichment of Dorea and Blautia; bacteria groups whose depletion has been reported in HIV-1 infected individuals in several other cohorts. Furthermore, HIV+ in our cohort exhibited a depletion of Prevotella, a genus whose enrichment has recently been shown in men having sex with men (MSM) regardless of HIV-1 status. The present study revealed the characteristics of dysbiotic fecal microbiome in HIV-1 infected adults in Ghana, a representative of West African populations.

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No evidence of colonization with community-acquired methicillin-resistant Staphylococcus aureus in HIV-1-infected men who have sex with men

Epidemiology and Infection ◽

10.1017/s0950268810000130 ◽

2010 ◽

Vol 138 (5) ◽

pp. 738-742 ◽

Cited By ~ 10

Author(s):

M. GIULIANI ◽

B. LONGO ◽

A. LATINI ◽

G. PRIGNANO ◽

M. MONACO ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Epidemiological Studies ◽

Cross Sectional Study ◽

Local Circulation ◽

Cross Sectional ◽

Methicillin Resistant ◽

The Usa ◽

Sex With Men ◽

Mrsa Colonization ◽

Hiv 1

SUMMARYTo assess the prevalence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) colonization in HIV-1-infected men who have sex with men (MSM), a cross-sectional study was conducted on 104 persons attending a large STI/HIV unit in Rome, Italy in the period June 2007–June 2008. Swabs obtained from both anterior nares and S. aureus isolates were characterized by phenotypic and genotypic methods. A total of 24 individuals (23·1%) were colonized with S. aureus but none carried MRSA. No statistically significant association between colonization with S. aureus and behavioural, clinical, virological or immunological characteristics was identified. This study indicates a lack of circulation of CA-MRSA in HIV-1-infected MSM in Italy and underscores large epidemiological differences between the USA and a European country, so that only locally conducted epidemiological studies can provide insight into the local circulation of CA-MRSA in general and selected populations.

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Rifaximin-Mediated Gut Microbiota Regulation Modulates the Polarization of Microglia During CUMS in Rat

10.21203/rs.3.rs-820698/v1 ◽

2021 ◽

Author(s):

Haonan Li ◽

Yujiao Xiang ◽

Zemeng Zhu ◽

Wei Wang ◽

Zhijun Jiang ◽

...

Keyword(s):

Fatty Acids ◽

Gut Microbiome ◽

Neuroprotective Effect ◽

Short Chain Fatty Acids ◽

Hippocampal Neurogenesis ◽

Short Chain ◽

Antidepressant Effect ◽

Mild Stress ◽

Fecal Microbiome ◽

Chain Fatty Acids

Abstract Background: Chronic unpredictable mild stress (CUMS) can not only lead to depression-like behavior but also change the composition of the gut microbiome. Regulating the gut microbiome can have an antidepressant effect, but the mechanism by which it improves depressive symptoms is not clear. Short-chain fatty acids (SCFAs) are small molecular compounds produced by the fermentation of non-digestible carbohydrates. SFCAs are ubiquitous in intestinal endocrine and immune cells, making them important mediators of gut microbiome-regulated body functions. Activated M1 microglia can cause pro-inflammatory and neurotoxic effects, while M2 microglia serve anti-inflammatory and neuroprotective functions. The balance between the two phenotypes of microglia plays an important role in the occurrence and treatment of depression caused by chronic stress. We hypothesized that rifaximin exerts an antidepressant effect by changing the abundance of fecal SFCA metabolites and transforming the microglial phenotype. Methods: We administered 150 mg/kg rifaximin intragastrically to rats exposed to CUMS for 4 weeks and investigated the composition of the fecal microbiome, the content of short-chain fatty acids in the serum and brain, microglial phenotypic profiles and hippocampal neurogenesis. Results: Our results show that rifaximin ameliorated depressive-like behavior induced by CUMS, as reflected by sucrose preference, the open field test and the Morris water maze. Rifaximin increased the relative abundance of Ruminococcaceae, which were significantly positively correlated with high levels of butyrate in the brain. Rifaximin also increased the transformation of M1 microglia into the M2 type in the hippocampal dentate gyrus (DG) and ameliorated neurogenic abnormalities and functional deficits caused by CUMS.Conclusions: These results suggest that rifaximin can enhance the neuroprotective effect of microglia to some extent by regulating the gut microbiome and one of its metabolites, butyrate.

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“La Familia” HIV prevention program: A focus on disclosure and family acceptance for Latino immigrant MSM to the USA

Salud Pública de México ◽

10.21149/spm.v55s4.5154 ◽

2013 ◽

Vol 55 (Supl.4) ◽

pp. 491 ◽

Cited By ~ 5

Author(s):

Rita M Melendez ◽

Jorge Zepeda ◽

Rafael Samaniego ◽

Deepalika Chakravarty ◽

Gabriela Alaniz

Keyword(s):

Sexual Orientation ◽

Hiv Prevention ◽

Prevention Program ◽

Control Group ◽

Structural Factors ◽

Latino Immigrant ◽

Before And After ◽

Family Acceptance ◽

The Usa ◽

Sex With Men

Objective. The objective of this study was to pilot test and evaluate a HIV prevention program that used a Freirean approach to engage Latino immigrant MSM (men who have sex with men) on issues of sexual orientation, family acceptance, stigma as well as HIV prevention and sexual risk behaviors. Materials and methods. Participants were evaluated using a survey before and after participation in the program and compared to a control group. Focus groups where participants discussed their experiences in the program as well as perceptions of the program were held and analyzed. Results. Survey results indicate that after their participation in the program, participants increased their safer sex behaviors, comfort disclosing their sexual orientation and support from friends. Conclusions. HIV prevention needs to incorporate cultural, social and structural factors.

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Antibacterial Monoclonal Antibodies Do Not Disrupt the Intestinal Microbiome or Its Function

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02347-19 ◽

2020 ◽

Vol 64 (5) ◽

Author(s):

Omari Jones-Nelson ◽

Andrey Tovchigrechko ◽

Matthew S. Glover ◽

Fiona Fernandes ◽

Udaya Rangaswamy ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Broad Spectrum ◽

Gut Microbiome ◽

Short Chain Fatty Acids ◽

Intestinal Microbiome ◽

Bacterial Metabolites ◽

Minimal Impact ◽

Fecal Microbiome ◽

Alpha And Beta Diversity ◽

Broad Spectrum Antibiotics

ABSTRACT Antibiotics revolutionized the treatment of infectious diseases; however, it is now clear that broad-spectrum antibiotics alter the composition and function of the host’s microbiome. The microbiome plays a key role in human health, and its perturbation is increasingly recognized as contributing to many human diseases. Widespread broad-spectrum antibiotic use has also resulted in the emergence of multidrug-resistant pathogens, spurring the development of pathogen-specific strategies such as monoclonal antibodies (MAbs) to combat bacterial infection. Not only are pathogen-specific approaches not expected to induce resistance in nontargeted bacteria, but they are hypothesized to have minimal impact on the gut microbiome. Here, we compare the effects of antibiotics, pathogen-specific MAbs, and their controls (saline or control IgG [c-IgG]) on the gut microbiome of 7-week-old, female, C57BL/6 mice. The magnitude of change in taxonomic abundance, bacterial diversity, and bacterial metabolites, including short-chain fatty acids (SCFA) and bile acids in the fecal pellets from mice treated with pathogen-specific MAbs, was no different from that with animals treated with saline or an IgG control. Conversely, dramatic changes were observed in the relative abundance, as well as alpha and beta diversity, of the fecal microbiome and bacterial metabolites in the feces of all antibiotic-treated mice. Taken together, these results indicate that pathogen-specific MAbs do not alter the fecal microbiome like broad-spectrum antibiotics and may represent a safer, more-targeted approach to antibacterial therapy.

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Changes of Human Gut Microbiome Correlated with Metabolomics After Cranberry Juice Consumption in a Double-Blinded, Placebo Controlled, Crossover Study

Current Developments in Nutrition ◽

10.1093/cdn/nzaa045_130 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 497-497

Author(s):

Shaomin Zhao ◽

Gary Wang ◽

Haiyan Liu ◽

Christina Khoo ◽

Liwei Gu

Keyword(s):

Gut Microbiome ◽

Alpha Diversity ◽

Short Chain Fatty Acids ◽

Cranberry Juice ◽

Microbial Composition ◽

Urine Metabolites ◽

Funding Sources ◽

Before And After ◽

Ocean Spray ◽

Double Blinded

Abstract Objectives 1) To investigate the changes of gut microbiome after 3 days and 21 days of cranberry juice consumption; 2) to correlate changes of microbiome with metabolome. Methods A double blinded, placebo-controlled, cross-over intervention study were conducted in 17 healthy young women aged 18–29 with normal BMI. Fecal, urine, and plasma samples were collected at baseline, after 3 days, and after 21 days consumption of double strength cranberry juice or a placebo juice. DNA was extracted from fecal samples and 16s rRNA was sequenced. Discriminant metabolites in urine and plasma was analyzed by UHPLC-Q-Orbitrap-HRMS and 0 identified using OPLS-DA models. Results 21-days but not 3 days of cranberry juice consumption significantly increased alpha diversity of colon microbiome compared to baseline. Significant increase in the abundance of Firmicutes, Ruminococcaceae, Faecalibacterium, and F/B (Firmicutes to Bacteroidetes) ratios were found after 21-days of cranberry juice intake. This was accompanied by decreases in Bacteroidetes, Proteobacteria, Clostridia, Enterobacteriaceae, Veillonellaceae, Bacteroides, Parabacteroides, and Enterobacter. Gut microbial composition before and after 21-days of cranberry juice consumption was significantly per Bray-Curtis dissimilarity analysis. However, cranberry consumption did not alter fecal content of short chain fatty acids, ammonia, or mucin. Spearman's correlation analysis showed significant positive or negative correlations between selected strains of bacteria and discriminant metabolites. 4-O-methylgallic acid was a discriminant metabolite in urine after 21-days of cranberry juice consumption. Its content positively correlated with Parabacteroides but negatively correlated with Faecalibacterium (P < 0.05). 3-(Hydroxyphenyl) propionic acid was a discriminant metabolite in plasma after cranberry juice consumption. Its content negatively correlated with Enterobacteriaceae (P < 0.05). Conclusions 21-days but not 3 days of cranberry juice consumption significantly altered colon microbiome. Correlation between gut bacteria and plasma, urine metabolites suggested interaction between gut microbiome and serum and urine metabolome. Funding Sources This research is funded in part by Ocean Spray Cranberries, inc.

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Glioma and temozolomide induced alterations in gut microbiome

Scientific Reports ◽

10.1038/s41598-020-77919-w ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Anthony Patrizz ◽

Antonio Dono ◽

Soheil Zorofchian ◽

Gabriella Hines ◽

Takeshi Takayasu ◽

...

Keyword(s):

Mouse Model ◽

Gut Microbiome ◽

Healthy Controls ◽

Fecal Samples ◽

Fecal Microbiome ◽

Therapeutic Modalities ◽

Microbial Dysbiosis ◽

Rrna Sequencing ◽

Before And After ◽

Immune Oncology

AbstractThe gut microbiome is fundamental in neurogenesis processes. Alterations in microbial constituents promote inflammation and immunosuppression. Recently, in immune-oncology, specific microbial taxa have been described to enhance the effects of therapeutic modalities. However, the effects of microbial dysbiosis on glioma are still unknown. The aim of this study was to explore the effects of glioma development and Temozolomide (TMZ) on fecal microbiome in mice and humans. C57BL/6 mice were implanted with GL261/Sham and given TMZ/Saline. Fecal samples were collected longitudinally and analyzed by 16S rRNA sequencing. Fecal samples were collected from healthy controls as well as glioma patients at diagnosis, before and after chemoradiation. Compared to healthy controls, mice and glioma patients demonstrated significant differences in beta diversity, Firmicutes/Bacteroides (F/B) ratio, and increase of Verrucomicrobia phylum and Akkermansia genus. These changes were not observed following TMZ in mice. TMZ treatment in the non-tumor bearing mouse-model diminished the F/B ratio, increase Muribaculaceae family and decrease Ruminococcaceae family. Nevertheless, there were no changes in Verrucomicrobia/Akkermansia. Glioma development leads to gut dysbiosis in a mouse-model, which was not observed in the setting of TMZ. These findings seem translational to humans and warrant further study.

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Microbial community with predictive power can be a new non-invasive substitute for clinical and pathological identification of diabetic nephropathy

10.21203/rs.3.rs-28863/v1 ◽

2020 ◽

Author(s):

Jin Shang ◽

Zhigang Ren ◽

Ang Li ◽

Ruixue Guo ◽

Yiding Zhang ◽

...

Keyword(s):

Diabetic Nephropathy ◽

Gut Microbiome ◽

Alpha Diversity ◽

Short Chain Fatty Acids ◽

Diagnostic Methods ◽

Microbial Composition ◽

Fecal Microbiome ◽

Non Invasive ◽

Microbial Biomarkers ◽

Functional Relevance

Abstract Background Diabetic nephropathy is characterized by increased incidence, deficient diagnostic methods and poor prognosis. New idea about altered gut microbiome associated with diagnosis and development of diabetic nephropathy remains to be verified. The major aim of our study is to relate fecal microbiome to clinically diagnosed diabetic kidney disease (DKD) or pathologically identified diabetic nephropathy (defined as DN) and further evaluate diagnosis potential of microbial markers for DKD/DN. We carried out 16S rRNA sequencing on a discovery cohort consisting of 352 patients (DKD = 120, DM = diabetes mellitus = 92, Con = healthy controls = 140) to identify microbial taxa and construct DKD classifier. Functional relevance and clinic correlation of microbiome changes were performed using PICRUSt and Spearman analysis, respectively. Independent 60 DKDs and 116 non-DKDs (DM = 46, Con = 70) were used to validate the results. The same analysis was performed on DKD pathologic subtypes (DN = 22, MN = membranous nephropathy = 22). Results DKD/DM samples had a distinct microbiome signature with lower alpha-diversity and significantly different microbial composition compared with Con (P < 0.001). Expansion of opportunistic pathogens (Peptostreptococcaceae_incertae_sedis, Clostridium_sensu_stricto_1, Streptococcus, Enterococcus, Erysipelotrichaceae_incertae_sedis), sulphate-reducing bacteria (Desulfovibrio) and depletion of bacteria producing short-chain fatty acids (SCFA) (Bacteroides, Faecalibacterium, Blautia and Roseburia) were major contributors to above differences. Interestingly, mucosa-associated bacteria including Akkermansia and Ruminococcus were also increased in DKD. The combination of 11 microbial markers could separate 120 DKDs from 232 non-DKDs with an area under curve (AUC) of 88.12%. Correspondingly, diagnostic power of microbial biomarkers was evaluated in a validation cohort of 60 patients and 116 non-DKDs (AUC = 79.75%). Besides DKD-related lipid and arginine metabolism, we also observed an increase of metabolism of aromatic amino acid in DM. Additionally, microbial comparison was carried out between pathologic subtypes of DKD, which could be used to distinguish DN from MN with 77.69% AUC. Conclusion Gut microbiome-related changes were associated with pathogenesis of DKD/DN; Microbiota-targeted markers could be an alternative test for DKD diagnosis and a non-invasive choice to differentiate DKD pathologic subtypes.

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