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

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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Consumption of a Western-style diet modulates the response of the murine gut microbiome to ciprofloxacin

10.1101/780049 ◽

2019 ◽

Author(s):

Damien J. Cabral ◽

Jenna I. Wurster ◽

Benjamin J. Korry ◽

Swathi Penumutchu ◽

Peter Belenky

Keyword(s):

Antibiotic Treatment ◽

Stress Responses ◽

Gut Microbiome ◽

Transcriptional Activity ◽

Control Diet ◽

Transcriptional Level ◽

Microbiome Composition ◽

Host Diet ◽

And Function ◽

The Impact

AbstractDietary composition and antibiotic use are known to 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 community structure and transcriptional activity. We found that mice consuming a Western-style diet experienced a greater expansion of Firmicutes following ciprofloxacin treatment than those eating a control diet. At the transcriptional level, we found that ciprofloxacin induced a reduction in the abundance of 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 shared response, we observed extensive differences in the response of the microbiota to ciprofloxacin on each diet. 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 key role in determining the extent of disruption of microbiome composition and function induced by antibiotic treatment.ImportanceWhile both diet and antibiotics are individually known to have profound impacts on gut microbiome composition, little work has been done to examine the effect of these two factors combined. A number of negative health outcomes, including diabetes and obesity, are associated with diets high in simple sugars in fats but low in host-indigestible fiber, and some of these outcomes may be mediated by the gut microbiome. Likewise, treatment with broad-spectrum antibiotics and the resulting dysbiosis is associated with many of the same detrimental side effects. Previous work has shown that nutrient availability, as influenced by host diet, plays an important role in determining the extent of antibiotic-induced disruption to the gut microbiome. Due to the growing incidence of disorders related to antibiotic-induced dysbiosis, it is essential to determine how the prevalence of high fat and sugar “Western”-style diets impacts the response of the microbiome to antibiotics.

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Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations

mSphere ◽

10.1128/msphere.00315-16 ◽

2017 ◽

Vol 2 (1) ◽

Cited By ~ 3

Author(s):

Jose Zaragoza ◽

Zachary Bendiks ◽

Charlotte Tyler ◽

Mary E. Kable ◽

Thomas R. Williams ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Community Dynamics ◽

Starter Culture ◽

Structure And Function ◽

Content Type ◽

Selective Pressures ◽

Spoilage Yeast ◽

And Function ◽

The Impact

ABSTRACT Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function. In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality. IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function.

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Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach

Viruses ◽

10.3390/v13091734 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1734

Author(s):

Janice Mayne ◽

Xu Zhang ◽

James Butcher ◽

Krystal Walker ◽

Zhibin Ning ◽

...

Keyword(s):

Food Chain ◽

Gut Microbiome ◽

Food Industry ◽

Ex Vivo ◽

Human Gut ◽

Microbiome Composition ◽

Human Gut Microbiome ◽

And Function ◽

The Impact

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

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Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Applied and Environmental Microbiology ◽

10.1128/aem.00956-12 ◽

2012 ◽

Vol 78 (17) ◽

pp. 6153-6160 ◽

Cited By ~ 56

Author(s):

Elizabeth A. Maga ◽

Prerak T. Desai ◽

Bart C. Weimer ◽

Nguyet Dao ◽

Dietmar Kültz ◽

...

Keyword(s):

Human Milk ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Gut Health ◽

Content Type ◽

Microbiome Composition ◽

The Impact ◽

Over Time

ABSTRACTHuman milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels ofFirmicutes(Clostridia) declined whereas those ofBacteroidetesincreased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P< 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (BifidobacteriaceaeandLactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae,Streptococcaceae,Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

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Temporal Measures in Cardiac Structure and Function During the Development of Obesity Induced by Different Types of Western Diet in a Rat Model

Nutrients ◽

10.3390/nu12010068 ◽

2019 ◽

Vol 12 (1) ◽

pp. 68 ◽

Cited By ~ 1

Author(s):

Danielle Fernandes Vileigas ◽

Cecília Lume de Carvalho Marciano ◽

Gustavo Augusto Ferreira Mota ◽

Sérgio Luiz Borges de Souza ◽

Paula Grippa Sant’Ana ◽

...

Keyword(s):

Cardiac Remodeling ◽

Systolic Function ◽

Control Diet ◽

Structure And Function ◽

Western Diet ◽

Cardiac Structure ◽

Different Types ◽

Cardiac Structure And Function ◽

And Function

Obesity is recognized worldwide as a complex metabolic disorder that has reached epidemic proportions and is often associated with a high incidence of cardiovascular diseases. To study this pathology and evaluate cardiac function, several models of diet-induced obesity (DIO) have been developed. The Western diet (WD) is one of the most widely used models; however, variations in diet composition and time period of the experimental protocol make comparisons challenging. Thus, this study aimed to evaluate the effects of two different types of Western diet on cardiac remodeling in obese rats with sequential analyses during a long-term follow-up. Male Wistar rats were distributed into three groups fed with control diet (CD), Western diet fat (WDF), and Western diet sugar (WDS) for 41 weeks. The animal nutritional profile and cardiac histology were assessed at the 41st week. Cardiac structure and function were evaluated by echocardiogram at four different moments: 17, 25, 33, and 41 weeks. A noninvasive method was performed to assess systolic blood pressure at the 33rd and 41st week. The animals fed with WD (WDF and WDS) developed pronounced obesity with an average increase of 86.5% in adiposity index at the end of the experiment. WDF and WDS groups also presented hypertension. The echocardiographic data showed no structural differences among the three groups, but WDF animals presented decreased endocardial fractional shortening and ejection fraction at the 33rd and 41st week, suggesting altered systolic function. Moreover, WDF and WFS animals did not present hypertrophy and interstitial collagen accumulation in the left ventricle. In conclusion, both WD were effective in triggering severe obesity in rats; however, only the WDF induced mild cardiac dysfunction after long-term diet exposure. Further studies are needed to search for an appropriate DIO model with relevant cardiac remodeling.

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Adverse physiologic effects of Western diet on right ventricular structure and function: role of lipid accumulation and metabolic therapy

Pulmonary Circulation ◽

10.1177/2045894018817741 ◽

2018 ◽

Vol 9 (1) ◽

pp. 204589401881774 ◽

Cited By ~ 4

Author(s):

Evan L. Brittain ◽

Megha Talati ◽

Niki Fortune ◽

Vineet Agrawal ◽

David F. Meoli ◽

...

Keyword(s):

Metabolic Syndrome ◽

Right Ventricular ◽

Diastolic Function ◽

Lipid Accumulation ◽

Systolic Pressure ◽

Structure And Function ◽

Western Diet ◽

And Function ◽

The Impact ◽

Rv Function

Little is known about the impact of metabolic syndrome (MS) on right ventricular (RV) structure and function. We hypothesized that mice fed a Western diet (WD) would develop RV lipid accumulation and impaired RV function, which would be ameliorated with metformin. Male C57/Bl6 mice were fed a WD or standard rodent diet (SD) for eight weeks. A subset of mice underwent pulmonary artery banding (PAB). Treated mice were given 2.5 g/kg metformin mixed in food. Invasive hemodynamics, histology, Western, and quantitative polymerase chain reaction (qPCR) were performed using standard techniques. Lipid content was detected by Oil Red O staining. Mice fed a WD developed insulin resistance, RV hypertrophy, and higher RV systolic pressure compared with SD controls. Myocardial lipid accumulation was greater in the WD group and disproportionately affected the RV. These structural changes were associated with impaired RV diastolic function in WD mice. PAB-WD mice had greater RV hypertrophy, increased lipid deposition, and lower RV ejection fraction compared with PAB SD controls. Compared to untreated mice, metformin lowered HOMA-IR and prevented weight gain in mice fed a WD. Metformin reduced RV systolic pressure, prevented RV hypertrophy, and reduced RV lipid accumulation in both unstressed stressed conditions. RV diastolic function improved in WD mice treated with metformin. WD in mice leads to an elevation in pulmonary pressure, RV diastolic dysfunction, and disproportionate RV steatosis, which are exacerbated by PAB. Metformin prevents the deleterious effects of WD on RV function and myocardial steatosis in this model of the metabolic syndrome.

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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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The Gut Microbiome in Neurodegenerative Disorders

The Oxford Handbook of the Microbiome-Gut-Brain Axis ◽

10.1093/oxfordhb/9780190931544.013.11 ◽

2020 ◽

Author(s):

Lindsay A. Euers ◽

Eamon M. M. Quigley

Keyword(s):

Nervous System ◽

Neurodegenerative Disorders ◽

Gut Microbiome ◽

Brain Structure ◽

Structure And Function ◽

Sufficient Evidence ◽

Brain Structure And Function ◽

The Many ◽

And Function ◽

The Impact

For some time, the concept of the gut-brain axis has served as a useful paradigm to explain the many interactions between the “big brain” (the central nervous system [CNS]) and the “little brain” (the enteric nervous system). Recently, the gut microbiome has been added to the equation and the proposition that gut microbes could influence brain structure and function and vice versa has emerged. Research in this field has been facilitated by dramatic progress in technologies that permit the delineation of the microbial constituents of the gut and their function in health and disease. Studies in a variety of animal models have amply supported the concept of a microbiota-gut-brain-axis and demonstrated that interventions that modulate the microbiome can influence animal behavior and CNS physiology. Understandably, studies of the impact of the microbiome on human brain structure and function are less numerous, but sufficient evidence does exist to indicate that this axis is operating in humans. In terms of neurodegenerative disorders, here again animal data dominate, but a sufficient body of evidence has accumulated to justify further explorations of the role of gut microbiota in Parkinson’s disease and Alzheimer’s disease, as well as in the aging process per se—“inflammaging.” Many confounding factors complicate the interpretation of human studies of the microbiome, and large, longitudinal studies that attempt to account for such confounders are needed. A number of interventions can be entertained—most notably, diet, probiotics, and prebiotics. To date, studies of any such interventions in neurodegenerative disease in humans are scanty.

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

Scientific Reports ◽

10.1038/s41598-021-87368-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

William Baiye Abange ◽

Casey Martin ◽

Aubin Joseph Nanfack ◽

Laeticia Grace Yatchou ◽

Nichole Nusbacher ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Gut Microbiome ◽

Alpha Diversity ◽

Structure And Function ◽

Fecal Microbiome ◽

Microbiome Composition ◽

And Function ◽

Living With Hiv ◽

Negative Controls ◽

Hiv Negative

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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