Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon

AbstractMultiple factors, such as immune disruption, prophylactic co-trimoxazole, and antiretroviral therapy, may influence the structure and function of the gut microbiome of children infected with HIV from birth. In order to understand whether HIV infection altered gut microbiome and to relate changes in microbiome structure and function to immune status, virological response and pediatric ART regimens, we characterized the gut microbiome of 87 HIV-infected and 82 non-exposed HIV-negative children from Yaounde, a cosmopolitan city in Cameroon. We found that children living with HIV had significantly lower alpha diversity in their gut microbiome and altered beta diversity that may not be related to CD4+ T cell count or viral load. There was an increased level of Akkermansia and Faecalibacterium genera and decreased level of Escherichia and other Gamma proteobacteria in children infected with HIV, among other differences. We noted an effect of ethnicity/geography on observed gut microbiome composition and that children on ritonavir-boosted protease inhibitor (PI/r)-based ART had gut microbiome composition that diverged more from HIV-negative controls compared to those on non-nucleoside reverse-transcriptase inhibitors-based ART. Further studies investigating the role of this altered gut microbiome in increased disease susceptibility are warranted for individuals who acquired HIV via mother-to-child transmission.

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Supplementation of Geranylgeraniol and Tocotrienols to High-Fat Diet Shifts the Gut Microbiome Composition and Function in Type 2 Diabetic Mice

Current Developments in Nutrition ◽

10.1093/cdn/nzaa045_026 ◽

2020 ◽

Vol 4 (Supplement_2) ◽

pp. 393-393

Author(s):

Moamen Elmassry ◽

Eunhee Chung ◽

Abdul Hamood ◽

Chwan-Li Shen

Keyword(s):

Relative Abundance ◽

Gut Microbiome ◽

High Fat Diet ◽

Alpha Diversity ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Microbiome Composition ◽

And Function

Abstract Objectives In recent years, characterization of gut microbiota composition and function were linked to the progression of type 2 diabetes mellitus. Recent evidence showed that Geranylgeraniol, an isoprenoid found in fruits, vegetables, and grains, improves glucose homeostasis. Similarly, Tocotrienols, a subfamily of vitamin E, also contains anti-diabetic properties. In this study, we examined the combined effect of geranylgeraniol and tocotrienols on the composition and function of gut microbiome in obese male mice. Methods Forty male C57BL/6J mice were assigned to 4 groups in a factorial design as follows: high-fat diet (HFD) (control group), HFD + geranylgeraniol [400 mg/kg diet] (GG group), HFD + tocotrienols [400 mg/kg diet] (TT group), and HFD + geranylgeraniol + tocotrienols (G + T group) for 14 weeks. 16S rRNA gene sequencing was done from cecal samples and microbiome and data analysis was performed with QIIME2 and PICRUSt2. Results Across all groups, the most abundant phyla were Verrucomicrobia, Firmicutes, Bacteroidetes, and Actinobacteria. There was no difference in alpha diversity among different groups. Different treatments influenced the relative abundance of certain bacteria. In the Bacteroidetes phylum, the relative abundance of family S24–7 increased in the TT group only. In the Firmicutes phylum, the relative abundance of family Lachnospiraceae was reduced upon the supplementation of geranylgeraniol or tocotrienols; individually or in combination. In Verrucomicrobia phylum, Akkermansia muciniphila relative abundance was reduced in the TT group but increased in the G + T group. The results of functional profiling of the gut microbiome revealed that geranylgeraniol supplementation caused an increase in the proportion of biosynthetic pathways related to purine, pyrimidine, and inosine-5’-phosphate and hexitol fermentation, and a decrease in the proportion of pathways involved in the biosynthesis of isoleucine, valine, histidine, arginine, and chorismate. The G + T group increased pathways related to thiamine diphosphate biosynthesis, and decreased others involved into sulfur oxidation and methylerythritol phosphate. Conclusions The influence of geranylgeraniol and tocotrienols supplementation on gut microbiome composition and function, suggests a prebiotic potential for the potential of geranylgeraniol and tocotrienols. Funding Sources American River Nutrition, LLC, Hadley, MA.

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Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin

mSystems ◽

10.1128/msystems.00317-20 ◽

2020 ◽

Vol 5 (4) ◽

Cited By ~ 1

Author(s):

Damien J. Cabral ◽

Jenna I. Wurster ◽

Benjamin J. Korry ◽

Swathi Penumutchu ◽

Peter Belenky

Keyword(s):

Gut Microbiome ◽

Transcriptional Activity ◽

Control Diet ◽

Structure And Function ◽

Western Diet ◽

Content Type ◽

Microbiome Composition ◽

Host Diet ◽

And Function ◽

The Impact

ABSTRACT Dietary composition and antibiotic use have major impacts on the structure and function of the gut microbiome, often resulting in dysbiosis. Despite this, little research has been done to explore the role of host diet as a determinant of antibiotic-induced microbiome disruption. Here, we utilize a multi-omic approach to characterize the impact of Western-style diet consumption on ciprofloxacin-induced changes to gut microbiome structure and transcriptional activity. We found that Western diet consumption dramatically increased Bacteroides abundances and shifted the community toward the metabolism of simple sugars and mucus glycoproteins. Mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. Transcriptionally, we found that ciprofloxacin reduced the abundance of tricarboxylic acid (TCA) cycle transcripts on both diets, suggesting that carbon metabolism plays a key role in the response of the gut microbiome to this antibiotic. Despite this, we observed extensive diet-dependent differences in the impact of ciprofloxacin on microbiota function. In particular, at the whole-community level we detected an increase in starch degradation, glycolysis, and pyruvate fermentation following antibiotic treatment in mice on the Western diet, which we did not observe in mice on the control diet. Similarly, we observed diet-specific changes in the transcriptional activity of two important commensal bacteria, Akkermansia muciniphila and Bacteroides thetaiotaomicron, involving diverse cellular processes such as nutrient acquisition, stress responses, and capsular polysaccharide (CPS) biosynthesis. These findings demonstrate that host diet plays a role in determining the impacts of ciprofloxacin on microbiome composition and microbiome function. IMPORTANCE Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how our “Western”-style diet impacts the response of the microbiome to antibiotics. While diet and antibiotics have profound impacts on gut microbiome composition, little work has been done to examine their combined effects. Previous work has shown that nutrient availability, influenced by diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Thus, we hypothesize that the Western diet will shift microbiota metabolism toward simple sugar and mucus degradation and away from polysaccharide utilization. Because of bacterial metabolism’s critical role in antibiotic susceptibility, this change in baseline metabolism will impact how the structure and function of the microbiome are impacted by ciprofloxacin exposure. Understanding how diet modulates antibiotic-induced microbiome disruption will allow for the development of dietary interventions that can alleviate many of the microbiome-dependent complications of antibiotic treatment.

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The gut microbiome is associated with brain structure and function in schizophrenia

Scientific Reports ◽

10.1038/s41598-021-89166-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shijia Li ◽

Jie Song ◽

Pengfei Ke ◽

Lingyin Kong ◽

Bingye Lei ◽

...

Keyword(s):

Gut Microbiome ◽

Brain Structure ◽

Gray Matter Volume ◽

Low Frequency ◽

Alpha Diversity ◽

Brain Regions ◽

Structure And Function ◽

Brain Structure And Function ◽

The Right ◽

And Function

AbstractThe effect of the gut microbiome on the central nervous system and its possible role in mental disorders have received increasing attention. However, knowledge about the relationship between the gut microbiome and brain structure and function is still very limited. Here, we used 16S rRNA sequencing with structural magnetic resonance imaging (sMRI) and resting-state functional (rs-fMRI) to investigate differences in fecal microbiota between 38 patients with schizophrenia (SZ) and 38 demographically matched normal controls (NCs) and explored whether such differences were associated with brain structure and function. At the genus level, we found that the relative abundance of Ruminococcus and Roseburia was significantly lower, whereas the abundance of Veillonella was significantly higher in SZ patients than in NCs. Additionally, the analysis of MRI data revealed that several brain regions showed significantly lower gray matter volume (GMV) and regional homogeneity (ReHo) but significantly higher amplitude of low-frequency fluctuation in SZ patients than in NCs. Moreover, the alpha diversity of the gut microbiota showed a strong linear relationship with the values of both GMV and ReHo. In SZ patients, the ReHo indexes in the right STC (r = − 0.35, p = 0.031, FDR corrected p = 0.039), the left cuneus (r = − 0.33, p = 0.044, FDR corrected p = 0.053) and the right MTC (r = − 0.34, p = 0.03, FDR corrected p = 0.052) were negatively correlated with the abundance of the genus Roseburia. Our results suggest that the potential role of the gut microbiome in SZ is related to alterations in brain structure and function. This study provides insights into the underlying neuropathology of SZ.

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Gut Microbiome Composition and Metabolomic Profiles of Wild and Captive Chinese Monals (Lophophorus Lhuysii)

10.21203/rs.3.rs-32587/v1 ◽

2020 ◽

Author(s):

Dandan Jiang ◽

Xin He ◽

Marc Valitutto ◽

Li Chen ◽

Qin Xu ◽

...

Keyword(s):

Gut Microbiome ◽

Bacterial Species ◽

Bird Species ◽

Alpha Diversity ◽

Integrated Approach ◽

Rrna Gene ◽

Metabolomic Profile ◽

Liquid Chromatograph ◽

Fecal Microbiome ◽

Microbiome Composition

Abstract Background：The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolomics of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal rRNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatograph (UHPLC) based metabolomics were used to examine the fecal microbiome composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial species in the two groups showed remarkable differences at all levels. Metabolomic profiling revealed a concurrent difference, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, these metabolites in difference are have a strong correlation with the main microbe in genus level.Conclusions: Various factors related to diet and environmental conditions played a crucial role in shaping the gut microbiome composition and metabolomic profile. Through this study, we have established a baseline for a normal gut microbiome and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive specimens has an impact on their overall health and reproduction.

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The Gut Microbiome Was Associated With Brain Structure and Function in Schizophrenia

10.21203/rs.3.rs-181659/v1 ◽

2021 ◽

Author(s):

Shijia Li ◽

Jie Song ◽

Pengfei Ke ◽

Lingyin Kong ◽

Bingye Lei ◽

...

Keyword(s):

Gut Microbiome ◽

Brain Structure ◽

Gray Matter Volume ◽

Low Frequency ◽

Alpha Diversity ◽

Brain Regions ◽

Structure And Function ◽

Brain Structure And Function ◽

The Right ◽

And Function

Abstract The effects of the gut microbiome on the central nervous system and its possible role in mental disorders have received increasing attention. However, our knowledge about the relationship between the gut microbiome and brain structure and function is still very limited. Here, we leveraged 16S rRNA sequencing with structural magnetic resonance imaging (sMRI) and resting-state functional (rs-fMRI) to investigate differences in fecal microbiota between 38 patients with schizophrenia (SZs) and 38 demographically matched normal controls (NCs) and explored whether such differences were associated with brain structure and function. At the genus level, we found that the relative abundance of Ruminococcus and Roseburia was significantly lower, whereas the abundance of Veillonella was increased in SZs compared to NCs. Additionally, the MRI results revealed that several brain regions showed lower gray matter volume (GMV) and regional homogeneity (ReHo), but increased amplitude of low-frequency fluctuation (ALFF) in SZs than in NCs. Statistical analyses were performed to explore the associations between microbial shifts and brain structure and function. Alpha diversity of gut microbiota showed a strong linear relationship with GMV and ReHo. Moreover, we found that lower ReHo indexes in the right STC (r = -0.35, p = 0.031, FDR corrected p = 0.039), the left cuneus (r = -0.33, p = 0.044, FDR corrected p = 0.053) and the right MTC (r = -0.34, p = 0.03, FDR corrected p = 0.052) were negatively correlated with a lower abundance of the genus Roseburia. This study suggests that the potential role of the gut microbiome in schizophrenia (SZ) is related to the alteration of brain structure and function, suggesting a new direction for studying the pathology of SZ.

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Virtualized Clinical Studies to Assess the Natural History and Impact of Gut Microbiome Modulation in Non-Hospitalized Patients with Mild to Moderate COVID-19 a Randomized, Open-Label, Prospective Study with a Parallel Group Study Evaluating the Physiologic Effects of KB109 on Gut Microbiota Structure and Function: A Structured Summary of a Study Protocol for a Randomized Controlled Study

10.21203/rs.3.rs-275217/v1 ◽

2021 ◽

Author(s):

John P Haran ◽

Jose C Pinero ◽

Yan Zheng ◽

Norma Alonzo-Palma ◽

Mark Wingertzahn

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Structure And Function ◽

Controlled Study ◽

Care Utilization ◽

Sample Collection ◽

Open Label ◽

Microbiome Composition ◽

And Function ◽

Microbiota Structure

Abstract Objectives These 2 parallel studies (K031 and K032) aim to evaluate the safety of KB109 in addition to supportive self-care (SSC) compared with SSC alone in outpatients with mild to moderate coronavirus disease 2019 (COVID-19). KB109 is a novel synthetic glycan that was formulated to modulate the gut microbiome composition and metabolic output in order to increase beneficial short-chain fatty acid (SCFA) production in the gut. The K031 study is designed to evaluate the safety of KB109 and characterize its impact on the natural progression of COVID-19 in patients with mild to moderate disease. The K032 study is evaluating the effect of KB109 on the gut microbiota structure and function in this same patient population. Additionally, both studies are evaluating measures of health care utilization, quality of life (QOL), laboratory indices, biomarkers of inflammation, and serological measures of immunity in patients who received SSC alone or with KB109. Noteworthy aspects of these outpatient studies include study design measures aimed at limiting in-person interactions to minimize the risk of infection spread, such as use of online diaries, telemedicine, and at-home sample collection.

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Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome

10.1101/2020.09.11.294447 ◽

2020 ◽

Author(s):

Olfat Khannous-Lleiffe ◽

Jesse R. Willis ◽

Ester Saus ◽

Ignacio Cabrera-Aguilera ◽

Isaac Almendros ◽

...

Keyword(s):

Heart Failure ◽

Gut Microbiome ◽

Alpha Diversity ◽

Antagonistic Effect ◽

Adverse Outcomes ◽

Sleep Fragmentation ◽

High Rate ◽

Fecal Microbiome ◽

Microbiome Composition ◽

The Individual

ABSTRACTHeart failure (HF) is a common condition associated with a high rate of hospitalizations and adverse outcomes. HF is characterized by impairments of the cardiac ventricular filling and/or ejection of blood capacity. Sleep fragmentation (SF) involves a series of short sleep interruptions that lead to fatigue and contribute to cognitive impairments and dementia. Both conditions are known to be associated with increased inflammation and dysbiosis of the gut microbiota. In the present study, male mice were distributed into four groups, and subjected for four weeks to either HF, SF, both HF and SF, or left unperturbed as controls. We used 16S metabarcoding to assess fecal microbiome composition before and after the experiments. Evidence for distinct alterations in several bacterial groups and an overall decrease in alpha diversity emerged in HF and SF treatment groups. Combined HF and SF conditions, however, showed no synergism, and observed changes were not always additive, suggesting that some of the individual effects of either HF or SF cancel each other out when applied concomitantly.IMPORTANCEThe study demonstrates the potential of the gut microbiome as a source of molecular markers for the diagnosis, prevention, and treatment of both heart failure and sleep fragmentation conditions in isolation. Our results provide the first evidence of an antagonistic effect of the presence of both conditions in the gut microbiome dysbiosis, showing an attenuation of the alterations that are observed when considering them separately.

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The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome

PeerJ ◽

10.7717/peerj.5494 ◽

2018 ◽

Vol 6 ◽

pp. e5494 ◽

Cited By ~ 2

Author(s):

Helen J. Dranse ◽

Ashlee Zheng ◽

André M. Comeau ◽

Morgan G.I. Langille ◽

Brian A. Zabel ◽

...

Keyword(s):

Knockout Mice ◽

Gut Microbiome ◽

Inflammatory Diseases ◽

Alpha Diversity ◽

Metabolic Phenotype ◽

Microbiome Composition ◽

Signalling Molecule ◽

Dramatic Difference ◽

And Function ◽

The Impact

Chemerin is an adipocyte derived signalling molecule (adipokine) that serves as a ligand activator of Chemokine-like receptor 1(CMKLR1). Chemerin/CMKLR1 signalling is well established to regulate fundamental processes in metabolism and inflammation. The composition and function of gut microbiota has also been shown to impact the development of metabolic and inflammatory diseases such as obesity, diabetes and inflammatory bowel disease. In this study, we assessed the microbiome composition of fecal samples isolated from wildtype, chemerin, or CMKLR1 knockout mice using Illumina-based sequencing. Moreover, the knockout mice and respective wildtype mice used in this study were housed at different universities allowing us to compare facility-dependent effects on microbiome composition. While there was no difference in alpha diversity within samples when compared by either facility or genotype, we observed a dramatic difference in the presence and abundance of numerous taxa between facilities. There were minor differences in bacterial abundance between wildtype and chemerin knockout mice, but significantly more differences in taxa abundance between wildtype and CMKLR1 knockout mice. Specifically, CMKLR1 knockout mice exhibited decreased abundance of Akkermansia and Prevotella, which correlated with body weight in CMKLR1 knockout, but not wildtype mice. This is the first study to investigate a linkage between chemerin/CMKLR1 signaling and microbiome composition. The results of our study suggest that chemerin/CMKLR1 signaling influences metabolic processes through effects on the gut microbiome. Furthermore, the dramatic difference in microbiome composition between facilities might contribute to discrepancies in the metabolic phenotype of CMKLR1 knockout mice reported by independent groups. Considered altogether, these findings establish a foundation for future studies to investigate the relationship between chemerin signaling and the gut microbiome on the development and progression of metabolic and inflammatory disease.

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Excess burden of age-associated comorbidities among people living with HIV in British Columbia, Canada: a population-based cohort study

BMJ Open ◽

10.1136/bmjopen-2020-041734 ◽

2021 ◽

Vol 11 (1) ◽

pp. e041734

Author(s):

Ni Gusti Ayu Nanditha ◽

Adrianna Paiero ◽

Hiwot M Tafessu ◽

Martin St-Jean ◽

Taylor McLinden ◽

...

Keyword(s):

British Columbia ◽

Cohort Study ◽

Population Based ◽

Age At Diagnosis ◽

Secondary Outcome ◽

People Living With Hiv ◽

Prevalence Trends ◽

Living With Hiv ◽

Negative Controls ◽

Hiv Negative

ObjectivesAs people living with HIV (PLWH) live longer, morbidity and mortality from non-AIDS comorbidities have emerged as major concerns. Our objective was to compare prevalence trends and age at diagnosis of nine chronic age-associated comorbidities between individuals living with and without HIV.Design and settingThis population-based cohort study used longitudinal cohort data from all diagnosed antiretroviral-treated PLWH and 1:4 age-sex-matched HIV-negative individuals in British Columbia, Canada.ParticipantsThe study included 8031 antiretroviral-treated PLWH and 32 124 HIV-negative controls (median age 40 years, 82% men). Eligible participants were ≥19 years old and followed for ≥1 year during 2000 to 2012.Primary and secondary outcome measuresThe presence of non-AIDS-defining cancers, diabetes, osteoarthritis, hypertension, Alzheimer’s and/or non-HIV-related dementia, cardiovascular, kidney, liver and lung diseases were identified from provincial administrative databases. Beta regression assessed annual age-sex-standardised prevalence trends and Kruskal-Wallis tests compared the age at diagnosis of comorbidities stratified by rate of healthcare encounters.ResultsAcross study period, the prevalence of all chronic age-associated comorbidities, except hypertension, were higher among PLWH compared with their community-based HIV-negative counterparts; as much as 10 times higher for liver diseases (25.3% vs 2.1%, p value<0.0001). On stratification by healthcare encounter rates, PLWH experienced most chronic age-associated significantly earlier than HIV-negative controls, as early as 21 years earlier for Alzheimer’s and/or dementia.ConclusionsPLWH experienced higher prevalence and earlier age at diagnosis of non-AIDS comorbidities than their HIV-negative controls. These results stress the need for optimised screening for comorbidities at earlier ages among PLWH, and a comprehensive HIV care model that integrates prevention and treatment of chronic age-associated conditions. Additionally, the robust methodology developed in this study, which addresses concerns on the use of administrative health data to measure prevalence and incidence, is reproducible to other settings.

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