Altered Gut Microbiota and Compositional Changes in Firmicutes and Proteobacteria in Mexican Undernourished and Obese Children

Functional foods lipids: unraveling their role in the immune response in obesity

Functional lipids are lipids that are found in food matrices and play an important role in influencing human health as their role goes beyond energy storage and structural components. Ongoing research into functional lipids has highlighted their potential to modulate immune responses and other mechanisms associated with obesity, along with its comorbidities. These lipids represent a new field that may offer new therapeutic and preventive strategies for these diseases by understanding their contribution to health. In this review, we discussed in-depth the potential food sources of functional lipids and their reported potential benefit of the major lipid classification: based on their composition such as simple, compound, and derived lipids, and based on their function such as storage and structural, by investigating the intricate mechanisms through which these lipids interact in the human body. We summarize the key insights into the bioaccessibility and bioavailability of the most studied functional lipids. Furthermore, we review the main immunomodulatory mechanisms reported in the literature in the past years. Finally, we discuss the perspectives and challenges faced in the food industry related to functional lipids.

Distinct gut flora profile induced by postnatal trans-fat diet in gestationally bisphenol A-exposed rats

There has been much evidence showing the repercussions of prenatal bisphenol A (BPA) exposure with a postnatal high fat-diet (HFD) on offspring's health. However, the information on how the interaction between these two variables affects the gut microbiome is rather limited. Hence, we investigated the impact of a postnatal trans fat diet (TFD) on the gut microbiome of offspring exposed to BPA during the prenatal period in an animal model. Pregnant rats were divided into 5 mg/kg/day BPA, vehicle Tween80 (P80) or control (CTL) drinking water until delivery (N = 6 per group). Then, weaned male pups were further subdivided into three normal diet (ND) groups (CTLND, P80ND, and BPAND) and three TFD groups (CTLTFD, P80TFD, and BPATFD) (n = 6 per group). 180-250 g of faecal samples were collected on days 50 and 100 to assess the composition of the offspring's intestinal flora using next-generation sequencing. The alpha diversity indices of TFD offspring with and without BPA were markedly lower than their ND counterparts (p<0.001-p<0.05). The beta diversity, hierarchical cluster and network analyses of the offspring's microbiome demonstrated that the microbiome species of the TFD group with and without BPA were distinctly different compared to the ND group. Consistently, TFD and ND offspring pairings exhibited a higher number of significantly different species (p<0.0001-p<0.05) compared to those exposed to prenatal BPA exposure and different life stages comparisons, as shown by the multivariate parametric analysis DESeq2. Predictive functional profiling of the offspring's intestinal flora demonstrated altered expressions of genes involved in metabolic pathways. In summary, the gut flora composition of the rat offspring may be influenced by postnatal diet instead of prenatal exposure to BPA. Our data indicate the possibility of perturbed metabolic functions and epigenetic modifications, in offspring that consumed TFD, which may theoretically lead to metabolic diseases in middle or late adulthood. Further investigation is necessary to fully understand these implications.

Multivariate Analysis and Correlation Study Shows the Impact of Anthropometric and Demographic Variables on Gut Microbiota in Obese Egyptian Children

Deciphering the gut microbiome's link to obesity is crucial. Our study characterized the gut microbial community in Egyptian children and investigated the effect of covariates on the gut microbiome, body mass index (BMI), geographical location, gender, and age. We used 16S rRNA sequencing to characterize the gut microbial communities of 49 children. We then evaluated these communities for diversity, potential biomarkers, and functional capacity. Alpha diversity of the non-obese group was higher than that of the obese group (Chao1, P = 0.006 and observed species, P = 0.003). Beta diversity analysis revealed significant variations in the gut microbiome between the two geographical locations, Cairo and Ismailia (unweighted UniFrac, P = 0.03) and between obesity statuses, obese and non-obese (weighted UniFrac, P = 0.034; unweighted UniFrac, P = 0.015). We observed a significantly higher Firmicutes/Bacteroidetes ratio in obese males than in non-obese males (P = 0.004). Interestingly, this difference was not seen in females (P = 0.77). Multivariable association with linear models (MaAsLin2) identified 8 microbial features associated with obesity, 12 associated with non-obesity, and found 29 and 13 features specific to Cairo and Ismailia patients, respectively. It has also shown one microbial feature associated with patients under five years old. MaAsLin2, however, failed to recognize any association between gender and the gut microbiome. Moreover, it could find the most predominant features in groups 2-9 but not in group 1. Another method used in the analysis is the Linear discriminant analysis Effect Size (LEfSe) approach, which effectively identified 19 biomarkers linked to obesity, 9 linked non-obesity, 20 linked to patients residing in Cairo, 14 linked to patients in Ismailia, one linked to males, and 12 linked to females. LEfSe could not, however, detect any prevalent bacteria among children younger or older than five. Future studies should take advantage of such correlations, specifically BMI, to determine the interventions needed for obesity management.

Systematic review of associations between gut microbiome composition and stunting in under-five children

Childhood stunting is associated with impaired cognitive development and increased risk of infections, morbidity, and mortality. The composition of the enteric microbiota may contribute to the pathogenesis of stunting. We systematically reviewed and synthesized data from studies using high-throughput genomic sequencing methods to characterize the gut microbiome in stunted versus non-stunted children under 5 years in LMICs. We included 14 studies from Asia, Africa, and South America. Most studies did not report any significant differences in the alpha diversity, while a significantly higher beta diversity was observed in stunted children in four out of seven studies that reported beta diversity. At the phylum level, inconsistent associations with stunting were observed for Bacillota, Pseudomonadota, and Bacteroidota phyla. No single genus was associated with stunted children across all 14 studies, and some associations were incongruent by specific genera. Nonetheless, stunting was associated with an abundance of pathobionts that could drive inflammation, such as Escherichia/Shigella and Campylobacter, and a reduction of butyrate producers, including Faecalibacterium, Megasphera, Blautia, and increased Ruminoccoccus. An abundance of taxa thought to originate in the oropharynx was also reported in duodenal and fecal samples of stunted children, while metabolic pathways, including purine and pyrimidine biosynthesis, vitamin B biosynthesis, and carbohydrate and amino acid degradation pathways, predicted linear growth. Current studies show that stunted children can have distinct microbial patterns compared to non-stunted children, which could contribute to the pathogenesis of stunting.

Gut microbiota and childhood malnutrition: Understanding the link and exploring therapeutic interventions

Childhood malnutrition is a metabolic condition that affects the physical and mental well-being of children and leads to resultant disorders in maturity. The development of childhood malnutrition is influenced by a number of physiological and environmental factors including metabolic stress, infections, diet, genetic variables, and gut microbiota. The imbalanced gut microbiota is one of the main environmental risk factors that significantly influence host physiology and childhood malnutrition progression. In this review, we have evaluated the gut microbiota association with undernutrition and overnutrition in children, and then the quantitative and qualitative significance of gut dysbiosis in order to reveal the impact of gut microbiota modification using probiotics, prebiotics, synbiotics, postbiotics, fecal microbiota transplantation, and engineering biology methods as new therapeutic challenges in the management of disturbed energy homeostasis. Understanding the host-microbiota interaction and the remote regulation of other organs and pathways by gut microbiota can improve the effectiveness of new therapeutic approaches and mitigate the negative consequences of childhood malnutrition.

Potential Mechanisms of Precision Nutrition-Based Interventions for Managing Obesity

Precision nutrition (PN) considers multiple individual-level and environmental characteristics or variables to better inform dietary strategies and interventions for optimizing health, including managing obesity and metabolic disorders. Here, we review the evidence on potential mechanisms-including ones to identify individuals most likely to respond-that can be leveraged in the development of PN interventions addressing obesity. We conducted a review of the literature and included laboratory, animal, and human studies evaluating biochemical and genetic data, completed and ongoing clinical trials, and public programs in this review. Our analysis describes the potential mechanisms related to 6 domains including genetic predisposition, circadian rhythms, physical activity and sedentary behavior, metabolomics, the gut microbiome, and behavioral and socioeconomic characteristics, i.e., the factors that can be leveraged to design PN-based interventions to prevent and treat obesity-related outcomes such as weight loss or metabolic health as laid out by the NIH 2030 Strategic Plan for Nutrition Research. For example, single nucleotide polymorphisms can modify responses to certain dietary interventions, and epigenetic modulation of obesity risk via physical activity patterns and macronutrient intake have also been demonstrated. Additionally, we identified limitations including questions of equitable implementation across a limited number of clinical trials. These include the limited ability of current PN interventions to address systemic influences such as supply chains and food distribution, healthcare systems, racial or cultural inequities, and economic disparities, particularly when designing and implementing PN interventions in low- and middle-income communities. PN has the potential to help manage obesity by addressing intra- and inter-individual variation as well as context, as opposed to "one-size fits all" approaches though there is limited clinical trial evidence to date.

Association of Pooled Fecal Microbiota on Height Growth in Children According to Enterotypes

OBJECTIVES

The association between fecal microbiota and height in children has yielded conflicting findings, warranting further investigation into potential differences in fecal bacterial composition between children with short stature and those of standard height based on enterotypes (ETs).

METHODS

According to the height z score for age and gender, the children were categorized into normal-stature (NS; n = 335) and short-stature (SS; n = 152) groups using a z score of -1.15 as a separator value. The human fecal bacterial FASTA/Q files (n = 487) were pooled and analyzed with the QIIME 2 platform with the National Center for Biotechnology Information alignment search tool. According to ETs, the prediction models by the machine learning algorithms were used for explaining SS, and their quality was validated.

RESULTS

The proportion of SS was 16.4% in ET Enterobacteriaceae (ET-E) and 68.1% in Prevotellaceae (ET-P). The Chao1 and Shannon indexes were significantly lower in the SS than in the NS groups only in ET-P. The fecal bacteria related to SS from the prediction models were similar regardless of ETs. However, in network analysis, the negative correlations between fecal bacteria in the NS and SS groups were much higher in the ET-P than in the ET-E. In the metagenome function, fecal bacteria showed an inverse association of biotin and secondary bile acid synthesis and downregulation of insulin/insulin-like growth factor-1-driven phosphoinositide 3-kinase Akt signaling and AMP-kinase signaling in the SS group compared with the NS group in both ETs.

CONCLUSION

The gut microbial compositions in children were associated with height. Strategies to modify and optimize the gut microbiota composition should be investigated for any potential in promoting height in children.

The Bern Birth Cohort (BeBiCo) to study the development of the infant intestinal microbiota in a high-resource setting in Switzerland: rationale, design, and methods

BACKGROUND

Microbiota composition is fundamental to human health with the intestinal microbiota undergoing critical changes within the first two years of life. The developing intestinal microbiota is shaped by maternal seeding, breast milk and its complex constituents, other nutrients, and the environment. Understanding microbiota-dependent pathologies requires a profound understanding of the early development of the healthy infant microbiota.

METHODS

Two hundred and fifty healthy pregnant women (≥20 weeks of gestation) from the greater Bern area will be enrolled at Bern University hospital's maternity department. Participants will be followed as mother-baby pairs at delivery, week(s) 1, 2, 6, 10, 14, 24, 36, 48, 96, and at years 5 and 10 after birth. Clinical parameters describing infant growth and development, morbidity, and allergic conditions as well as socio-economic, nutritional, and epidemiological data will be documented. Neuro-developmental outcomes and behavior will be assessed by child behavior checklists at and beyond 2 years of age. Maternal stool, milk, skin and vaginal swabs, infant stool, and skin swabs will be collected at enrolment and at follow-up visits. For the primary outcome, the trajectory of the infant intestinal microbiota will be characterized by 16S and metagenomic sequencing regarding composition, metabolic potential, and stability during the first 2 years of life. Secondary outcomes will assess the cellular and chemical composition of maternal milk, the impact of nutrition and environment on microbiota development, the maternal microbiome transfer at vaginal or caesarean birth and thereafter on the infant, and correlate parameters of microbiota and maternal milk on infant growth, development, health, and mental well-being.

DISCUSSION

The Bern birth cohort study will provide a detailed description and normal ranges of the trajectory of microbiota maturation in a high-resource setting. These data will be compared to data from low-resource settings such as from the Zimbabwe-College of Health-Sciences-Birth-Cohort study. Prospective bio-sampling and data collection will allow studying the association of the microbiota with common childhood conditions concerning allergies, obesity, neuro-developmental outcomes , and behaviour. Trial registration The trial has been registered at www.

CLINICALTRIALS

gov , Identifier: NCT04447742.

Exploring Gut Microbiota and the Influence of Physical Activity Interventions on Overweight and Obese Children and Adolescents: A Systematic Review

The recognition that the gut microbiota of obese children differs from lean children has grown, and some studies suggest that physical activity positively influences the gut microbiota. This systematic review explores the changes in the gut microbiota composition of obese and non-obese children and adolescents and provides an understanding of the effects of physical activity interventions in modulating their microbiota. The PRISMA protocol was used across PubMed, Scopus, and Web of Science. Overall, twenty-four research papers were included in accordance with the chosen inclusion and exclusion criteria, eighteen studies compared the gut microbiota of obese and normal-weight children and adolescents, and six studies explored the effect of physical activity interventions on the gut microbiota. The analysis indicated that obese gut microbiota is reduced in Bacteroidetes, Bifidobacterium and alpha diversity but enriched in Proteobacteria and Lactobacillus. Interventions with physical activity seem to improve the alpha diversity and beneficial bacteria linked to body weight loss in children and adolescents. The gut microbiota of obese children exhibited a remarkably individual variation. More interventions are needed to clearly and accurately explore the relationships between child obesity, gut microbiota, and physical activity and to develop approaches to decrease the incidence of paediatric obesity.

Gut microbial composition and functionality of school-age Mexican population with metabolic syndrome and type-2 diabetes mellitus using shotgun metagenomic sequencing

Gut metagenome in pediatric subjects with metabolic syndrome (MetS) and type-2 diabetes mellitus (T2DM) has been poorly studied, despite an alarming worldwide increase in the prevalence and incidence of obesity and MetS within this population. The objective of this study was to characterize the gut microbiome taxonomic composition of Mexican pediatric subjects with MetS and T2DM using shotgun metagenomics and analyze the potential relationship with metabolic changes and proinflammatory effects. Paired-end reads of fecal DNA samples were obtained through the Illumina HiSeq X Platform. Statistical analyses and correlational studies were conducted using gut microbiome data and metadata from all individuals. Gut microbial dysbiosis was observed in MetS and T2DM children compared to healthy subjects, which was characterized by an increase in facultative anaerobes (i.e., enteric and lactic acid bacteria) and a decrease in strict anaerobes (i.e., Erysipelatoclostridium, Shaalia, and Actinomyces genera). This may cause a loss of gut hypoxic environment, increased gut microbial nitrogen metabolism, and higher production of pathogen-associated molecular patterns. These metabolic changes may trigger the activation of proinflammatory activity and impair the host's intermediate metabolism, leading to a possible progression of the characteristic risk factors of MetS and T2DM, such as insulin resistance, dyslipidemia, and an increased abdominal circumference. Furthermore, specific viruses (Jiaodavirus genus and Inoviridae family) showed positive correlations with proinflammatory cytokines involved in these metabolic diseases. This study provides novel evidence for the characterization of MetS and T2DM pediatric subjects in which the whole gut microbial composition has been characterized. Additionally, it describes specific gut microorganisms with functional changes that may influence the onset of relevant health risk factors.

Early Life Factors Influencing Children Gut Microbiota at 3.5 Years from Two French Birth Cohorts

Early life gut microbiota-influencing factors may play an important role in programming individuals long-term health and substantial efforts have been devoted into studying the development of the gut microbiota in relation to early life events. This study aimed to examine in a single study, the persistence of associations between 20 factors occurring in the early life and the gut microbiota at 3.5 years of 798 children from two French nationwide birth cohorts, EPIPAGE 2 (very preterm children) and ELFE (late preterm and full-term children). Gut microbiota profiling was assessed using 16S rRNA gene sequencing-based method. Upon thorough adjustment of confounding factors, we demonstrated that gestational age was one of the factors most associated with gut microbiota differences with a noticeable imprint of prematurity at 3.5 years of age. Children born by cesarean section harbored lower richness and diversity and a different overall gut microbiota composition independently of preterm status. Children who had ever received human milk were associated with a Prevotella-driven enterotype (P_type) compared to those who had never received human milk. Living with a sibling was associated with higher diversity. Children with siblings and those attending daycare centers were associated with a P_type enterotype. Maternal factors including the country of birth and preconception maternal body mass index were associated with some microbiota characteristics: children born to overweight or obese mothers showed increased gut microbiota richness. This study reveals that multiple exposures operating from early life imprint the gut microbiota at 3.5 years that is a pivotal age when the gut microbiota acquires many of its adult characteristics.

Polyhalogenated carbazoles induce hepatic metabolic disorders in mice via alteration in gut microbiota

Polyhalogenated carbazoles (PHCZs) have been widely accepted as emerging pollutants, whereas their ecological and health risks remain uncertain. Herein, female and male Sprague-Dawley (SD) mice were treated with four typical PHCZs to investigate their negative consequences, along with alternations in gut microbiota to indicate underlying mechanisms. In female mice, the relative liver weight ratio increased after four PHCZs exposure; 2-bromocarbazole (2-BCZ) increased urine glucose level; 3-bromocarbazole (3-BCZ) decreased the glucose and total cholesterol levels; 3,6-dichlorocarbazole (3,6-DCCZ) decreased glucose level. The only disturbed biochemical index in male mice was the promoted alkaline phosphatase (ALP) level by 3,6-DCCZ. We also found that the differential blood biochemical indices were correlated with gut microbiota. 3-BCZ and 3,6-DCCZ altered Bacteroidetes and Proteobacteria phyla in female and male mice, which were correlated with metabolic disorders. Our findings demonstrated the correlation between PHCZs induced potential hepatotoxicity and metabolic disorders may be due to their dioxin-like potentials and endocrine disrupting activities, and the gender differences might result from their estrogenic activities. Overall, data presented here can help to evaluate the ecological and health risks of PHCZs and reveal the underlying mechanisms.

Role of Dietary Fiber and Energy Intake on Gut Microbiome in Vegans, Vegetarians, and Flexitarians in Comparison to Omnivores-Insights from the Nutritional Evaluation (NuEva) Study

In recent years, there has been a global trend towards a plant-based lifestyle. In the NuEva study, dietary self-reports of 258 participants following one of four diets (Western diet (WD), flexitarians (Flex), vegetarians (VG), and vegans (VN)) were related to fecal microbiome composition. Reduced consumption of animal products (VN < VG < Flex < WD) was associated with a decreased intake of energy (p < 0.05), and an increased intake of soluble and non-soluble dietary fibers (p < 0.05). We observed the lowest average microbiome diversity in vegans and the highest in WD. Compared to WD, VG (p < 0.05) and VN (p < 0.01) differed significantly in their bacterial composition. These data were related to dietary fiber intake. Furthermore, we identified 14 diet-specific biomarkers at the genus level by using LefSe analysis. Of these, 11 showed minimum or maximum counts in WD or VN. While the VN-specific species were inversely associated with cardiovascular risk factors, a positive association was detected for the WD-specific species. Identifying biomarkers for the diets on extreme ends of the spectrum (WD and VN) and their association with cardiovascular risk factors provides a solid evidence base highlighting the potential and the need for the development of personalized recommendations dependent on dietary patterns. Even so, the mechanisms underlying these diet-specific differences in microbiome composition cannot yet be clearly assessed. The elucidation of these associations will provide the basis for personalized nutritional recommendations based on the microbiome.

Longitudinal Analysis of the Intestinal Microbiota among a Cohort of Children in Rural and Urban Areas of Pakistan

The profile of the intestinal microbiota is known to be altered in malnourished young children in low- and middle-income countries. However, there are limited studies longitudinally evaluating the intestinal microbiota in malnourished young children in resource-limited settings over the first two years of life. In this longitudinal pilot study, we determined the effect of age, residential location, and intervention on the composition, relative abundance, and diversity of the intestinal microbiota in a representative sample of children under 24 months of age with no diarrhea in the preceding 72 h in the urban and rural areas of Sindh, Pakistan nested within a cluster-randomized trial evaluating the effect of zinc and micronutrients on growth and morbidity (ClinicalTrials.gov Identifier: NCT00705445). The major findings were age-related with significant changes in alpha and beta diversity with increasing age. There was a significant increase in the relative abundance of the Firmicutes and Bacteroidetes phyla and a significant decrease in that of the Actinobacteria and Proteobacteria phyla (p < 0.0001). There were significant increases in the relative abundances of the major genera Bifidobacterium, Escherichia/Shigella and Streptococcus (p < 0.0001), and no significant change in the relative abundance of Lactobacillus. Using the LEfSE algorithm, differentially abundant taxa were identified between children in the first and second years of age, between those residing in rural and urban areas, and those who received different interventions at different ages from 3 to 24 months. The numbers of malnourished (underweight, wasted, stunted) or well-nourished children at each age, in each intervention arm, and at urban or rural sites were too small to determine if there were significant differences in alpha or beta diversity or differentially abundant taxa among them. Further longitudinal studies with larger numbers of well-nourished and malnourished children are required to fully characterize the intestinal microbiota of children in this region.

Cellular and Molecular Mechanisms Associating Obesity to Bone Loss

Obesity is an alarming disease that favors the upset of other illnesses and enhances mortality. It is spreading fast worldwide may affect more than 1 billion people by 2030. The imbalance between excessive food ingestion and less energy expenditure leads to pathological adipose tissue expansion, characterized by increased production of proinflammatory mediators with harmful interferences in the whole organism. Bone tissue is one of those target tissues in obesity. Bone is a mineralized connective tissue that is constantly renewed to maintain its mechanical properties. Osteoblasts are responsible for extracellular matrix synthesis, while osteoclasts resorb damaged bone, and the osteocytes have a regulatory role in this process, releasing growth factors and other proteins. A balanced activity among these actors is necessary for healthy bone remodeling. In obesity, several mechanisms may trigger incorrect remodeling, increasing bone resorption to the detriment of bone formation rates. Thus, excessive weight gain may represent higher bone fragility and fracture risk. This review highlights recent insights on the central mechanisms related to obesity-associated abnormal bone. Publications from the last ten years have shown that the main molecular mechanisms associated with obesity and bone loss involve: proinflammatory adipokines and osteokines production, oxidative stress, non-coding RNA interference, insulin resistance, and changes in gut microbiota. The data collection unveils new targets for prevention and putative therapeutic tools against unbalancing bone metabolism during obesity.

Oral Exposure to Polystyrene Microplastics of Mice on a Normal or High-Fat Diet and Intestinal and Metabolic Outcomes

BACKGROUND

Microplastics (MPs) are small particles of plastic (≤5mm in diameter). In recent years, oral exposure to MPs in living organisms has been a cause of concern. Leaky gut syndrome (LGS), associated with a high-fat diet (HFD) in mice, can increase the entry of foreign substances into the body through the intestinal mucosa.

OBJECTIVES

We aimed to evaluate the pathophysiology of intestinal outcomes associated with consuming a high-fat diet and simultaneous intake of MPs, focusing on endocrine and metabolic systems.

METHODS

C57BL6/J mice were fed a normal diet (ND) or HFD with or without polystyrene MP for 4 wk to investigate differences in glucose tolerance, intestinal permeability, gut microbiota, as well as metabolites in serum, feces, and liver.

RESULTS

In comparison with HFD mice, mice fed the HFD with MPs had higher blood glucose, serum lipid concentrations, and nonalcoholic fatty liver disease (NAFLD) activity scores. Permeability and goblet cell count of the small intestine (SI) in HFD-fed mice were higher and lower, respectively, than in ND-fed mice. There was no obvious difference in the number of inflammatory cells in the SI lamina propria between mice fed the ND and mice fed the ND with MP, but there were more inflammatory cells and fewer anti-inflammatory cells in mice fed the HFD with MPs in comparison with mice fed the HFD without MPs. The expression of genes related to inflammation, long-chain fatty acid transporter, and Na+/glucose cotransporter was significantly higher in mice fed the HFD with MPs than in mice fed the HFD without MPs. Furthermore, the genus Desulfovibrio was significantly more abundant in the intestines of mice fed the HFD with MPs in comparison with mice fed the HFD without MPs. Muc2 gene expression was decreased when palmitic acid and microplastics were added to the murine intestinal epithelial cell line MODE-K cells, and Muc2 gene expression was increased when IL-22 was added.

DISCUSSION

Our findings suggest that in this study, MP induced metabolic disturbances, such as diabetes and NAFLD, only in mice fed a high-fat diet. These findings suggest that LGS might have been triggered by HFD, causing MPs to be deposited in the intestinal mucosa, resulting in inflammation of the intestinal mucosal intrinsic layer and thereby altering nutrient absorption. These results highlight the need for reducing oral exposure to MPs through remedial environmental measures to improve metabolic disturbance under high-fat diet conditions. https://doi.org/10.1289/EHP11072.

Metabolite profiling of human-originated Lachnospiraceae at the strain level

The human gastrointestinal (GI) tract harbors diverse microbes, and the family Lachnospiraceae is one of the most abundant and widely occurring bacterial groups in the human GI tract. Beneficial and adverse effects of the Lachnospiraceae on host health were reported, but the diversities at species/strain levels as well as their metabolites of Lachnospiraceae have been, so far, not well documented. In the present study, we report on the collection of 77 human-originated Lachnospiraceae species (please refer hLchsp, https://hgmb.nmdc.cn/subject/lachnospiraceae) and the in vitro metabolite profiles of 110 Lachnospiraceae strains (https://hgmb.nmdc.cn/subject/lachnospiraceae/metabolites). The Lachnospiraceae strains in hLchsp produced 242 metabolites of 17 categories. The larger categories were alcohols (89), ketones (35), pyrazines (29), short (C2-C5), and long (C > 5) chain acids (31), phenols (14), aldehydes (14), and other 30 compounds. Among them, 22 metabolites were aromatic compounds. The well-known beneficial gut microbial metabolite, butyric acid, was generally produced by many Lachnospiraceae strains, and Agathobacter rectalis strain Lach-101 and Coprococcus comes strain NSJ-173 were the top 2 butyric acid producers, as 331.5 and 310.9 mg/L of butyric acids were produced in vitro, respectively. Further analysis of the publicly available cohort-based volatile-metabolomic data sets of human feces revealed that over 30% of the prevailing volatile metabolites were covered by Lachnospiraceae metabolites identified in this study. This study provides Lachnospiraceae strain resources together with their metabolic profiles for future studies on host-microbe interactions and developments of novel probiotics or biotherapies.

Impact of Lactobacillus-originated metabolites on enterohemorrhagic E. coli in rumen fluid

Rumen is one of the richest microbial ecosystems naturally harboring many zoonotic pathogens. Controlling the colonization of cattle originated zoonotic pathogens in rumen, particularly enterohemorrhagic Escherichia coli (EHEC), is critical in reducing foodborne enteric diseases in humans. In this study, we aimed to inhibit the growth of EHEC in a simulated rumen system with collected rumen fluids (RFs) using live probiotics, synbiotics, and their metabolites. EHEC inoculated RF was treated with live wild type Lactobacillus casei (LCwt), LCwt with 0.5% peanut flour (LCwt+PF), an engineered LC capable of overexpressing linoleate isomerase (LCCLA), and their metabolites collected in cell-free culture supernatants (CFCSwt, CFCSwt+PF, and CFCSCLA) at various time points. A growth stimulatory effect toward Lactobacillus spp. was exerted by all CFCS, while the EHEC was suppressed. Among other treatments only LCwt+PF reduced EHEC by 2.68 logs after 72 h. This observation was also supported by metataxonomic analysis. A reduction in Bacteroidetes and Proteobacteria while increase in Firmicutes was observed at 48 h by the presence of CFCSs as compared to the control. Our observation implies probiotic-originated metabolites modulate rumen microbiota positively which can be deployed to control the transmission of cattle-borne pathogens specifically EHEC.

Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel

The gut microbiome is important for host nutrient metabolism and ecological adaptation. However, how the gut microbiome is affected by host phylogeny, ecology and diet during sympatric speciation remain unclear. Here, we compare and contrast the gut microbiome of two sympatric blind mole rat species and correlate them with their corresponding host phylogeny, ecology soil metagenomes, and diet to determine how these factors may influence their gut microbiome. Our results indicate that within the host microbiome there is no significant difference in community composition, but the functions between the two sympatric species populations vary significantly. No significant correlations were found between the gut microbiome differentiation and their corresponding ecological soil metagenomes and host phylogeny. Functional enrichment analysis suggests that the host diets may account for the functional divergence of the gut microbiome. Our results will help us understand how the gut microbiome changes with corresponding ecological dietary factors in sympatric speciation of blind subterranean mole rats.

Nutritional composition, heavy metal content and in vitro effect on the human gut microbiota of Talitrus saltator, an underutilized crustacean from the Atlantic coast

In this study, an undervalued marine crustacean (Talitrus saltator) was characterized in terms of nutritional and heavy metal composition and its potential to affect human gut microbiota. Nutritional analysis of this crustacean revealed that it complies with the criteria established in European legislation to include nutritional claims in their labeling, such as "source of fiber," "low in fat," "low in sugars" and "high in protein." The analysis of the heavy metal content did not reveal any risk derived from the presence of Cd, Hg, or Pb, whereas essential metals contained in 100 g exceeded the minimum daily requirements recommended in Europe for Zn (19.78 mg/kg), Cu (2.28 mg/kg), and Fe (32.96 mg/kg). Using an in vitro system, the effect of T. saltator on the human colonic microbiota shows some beneficial effects, such as fermentation-maintained populations of Bifidobacterium or Lactobacillus, did not increase Firmicutes phylum counts, decreased the Firmicutes/Bacteroidetes ratio, and stimulated 11 metabolic pathways with respect to baseline. These results are unusual in a high protein content-food. However, negative effects were also found in gut microbiota relative proportions, such as an increase in the Proteobacteria phylum and especially some opportunistic bacteria from this phylum, probably due to the antimicrobial effect of chitin on other groups more sensitive to its effect. This work shows for the first time the effect of T. saltator on human colonic microbiota using and in vitro system. The presence of chitin in its composition could provide some beneficial effects by modulating the microbiota, but as T. saltator is a high-protein food, more studies should be carried out showing these benefits.

Importance of Microbiome of Fecal Samples Obtained from Adolescents with Different Weight Conditions on Resistance Gene Transfer

Antimicrobial resistance (AMR) is a relevant public health problem worldwide, and microbiome bacteria may contribute to the horizontal gene transfer associated with antimicrobial resistance. The microbiome of fecal samples from Mexican adolescents were analyzed and correlated with eating habits, and the presence of AMR genes on bacteria in the microbiome was evaluated. Fecal samples from adolescents were collected and processed to extract genomic DNA. An Illumina HiSeq 1500 system was used to determine resistance genes and the microbiome of adolescents through the amplification of gene resistance and the V3–V4 regions of RNA, respectively. Analysis of the microbiome from fecal samples taken from 18 obese, overweight, and normal-weight adolescents revealed that the Firmicutes was the most frequent phylum, followed by Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. The following species were detected as the most frequent in the samples: F. prausnitzii, P. cori, B. adolescentis, E. coli and A. muciniphila. The presence of Bacteroides, Prevotella and Ruminococcus was used to establish the enterotype; enterotype 1 was more common in women and enterotype 2 was more common in men. Twenty-nine AMR genes were found for β-lactamases, fluoroquinolones, aminoglycosides, macrolide, lincosamides, streptogramin (MLS), tetracyclines and sulfonamides. The presence of microorganisms in fecal samples that harbor AMR genes that work against antimicrobials frequently used for the treatment of microbial infections such as b-lactams, macrolides, aminoglycosides, MLS, and tetracyclines is of great concern, as these organisms may be an important reservoir for horizontal AMR gene transfer.

Dynamic Population of Gut Microbiota as an Indicator of Inflammatory Bowel Disease

Background

Inflammatory bowel disease is a chronic inflammatory disease of the gastrointestinal tract. The gut microbiota is an important factor in the pathogenesis of inflammatory bowel disease (IBD). Due to a link between the gut microbiota and IBD, studying microbiota changes using an accurate, sensitive and rapid method for detection of the disease seems necessary. This study aimed to compare the composition of gut microbiota in three groups of people, including IBD patients, cured Inflammatory bowel disease (CIBD), and healthy groups.

Methods

For this study, 45 stool samples (15 from each group) were collected. Using real-time PCR, the abundance of 11 bacterial 16S rRNA gene sequences was examined.

Results

In the IBD group, the number of three bacterial phyla, including Firmicutes, Actinobacteria, and Bacteroidetes, decreased (p < 0.01, p < 0.01, and p < 0.001, respectively), while the population of γ-Proteobacteria increased significantly (p < 0.0001). In the CIBD group, the number of Actinobacteria enhanced (p < 0.01), but that of Bacteroidetes and Firmicutes decreased (p < 0.01, and p < 0.05, respectively).

Conclusion

Findings of this study indicate that decrease in Firmicutes and increase in γ-Proteobacteria could be used as an indicator of IBD instead of employing invasive and costly detection methods such as colonoscopy and other tests.

Gut Microbiota Composition in Undernourished Children Associated with Diet and Sociodemographic Factors: A Case–Control Study in Indonesia

Malnutrition, which consists of undernutrition and overnutrition, is associated with gut microbiota composition, diet, and sociodemographic factors. Undernutrition is a nutrient deficiency that that should be identified to prevent other diseases. In this study, we evaluate the gut microbiota composition in undernourished children in association with diet and sociodemographic factors. We observed normal children (n= 20) and undernourished children (n= 20) for ten days in Lombok and Yogyakarta. Diet, sociodemographic factors, and medical records were recorded using food records, screening forms, and standard household questionnaires. Gut microbiota analysis was performed using 16S rRNA gene sequencing targeting the V3–V4 region. The result showed that the undernourished group had lower energy intake. In addition, the undernourished group had lower quality of medical records, parent knowledge, education, and exclusive breastfeeding. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia were significantly different between normal and undernourished children. Based on LefSe, we determined that Akkermansia is a biomarker for undernourished children. In conclusion, diet and sociodemographic factors affect the gut microbiota composition of undernourished children.

Adaptation and Resistance: How Bacteroides thetaiotaomicron Copes with the Bisphenol A Substitute Bisphenol F

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome. The highly abundant human commensal bacterium Bacteroides thetaiotaomicron was exposed to bisphenols (Bisphenol A (BPA), Bisphenol F (BPF), Bisphenol S (BPS)), to examine the mode of action, in particular of BPF. All chemicals caused a concentration-dependent growth inhibition and the half-maximal effective concentration (EC50) corresponded to their individual logP values, a measure of their hydrophobicity. B. thetaiotaomicron exposed to BPF decreased membrane fluidity with increasing BPF concentrations. Physiological changes including an increase of acetate concentrations were observed. On the proteome level, a higher abundance of several ATP synthase subunits and multidrug efflux pumps suggested an increased energy demand for adaptive mechanisms after BPF exposure. Defense mechanisms were also implicated by a pathway analysis that identified a higher abundance of members of resistance pathways/strategies to cope with xenobiotics (i.e., antibiotics). Here, we present further insights into the mode of action of bisphenols in a human commensal gut bacterium regarding growth inhibition, and the physiological and functional state of the cell. These results, combined with microbiota-directed effects, could lead to a better understanding of host health disturbances and disease development based on xenobiotic uptake.

Gut microbial characteristics in poor appetite and undernutrition: a cohort of older adults and microbiota transfer in germ-free mice

BACKGROUND

Older adults are particularly prone to the development of poor appetite and undernutrition. Possibly, this is partly due to the aged gut microbiota. We aimed to evaluate the gut microbiota in relation to both poor appetite and undernutrition in community-dwelling older adults. Furthermore, we studied the causal effects of the microbiota on body weight and body composition by transferring faecal microbiota from cohort participants into germ-free mice.

METHODS

First, we conducted a cross-sectional cohort study of 358 well-phenotyped Dutch community-dwelling older adults from the Longitudinal Aging Study Amsterdam. Data collection included body measurements, a faecal and blood sample, as well as extensive questionnaires on appetite, dietary intake, and nutritional status. Appetite was assessed by the Council of Nutrition Appetite Questionnaire (CNAQ) and undernutrition was defined by either a low body mass index (BMI) (BMI < 20 kg/m² if <70 years or BMI < 22 kg/m² if ≥70 years) or >5% body weight loss averaged over the last 2 years. Gut microbiota composition was determined with 16S rRNA sequencing. Next, we transferred faecal microbiota from 12 cohort participants with and without low BMI or recent weight loss into a total of 41 germ-free mice to study the potential causal effects of the gut microbiota on host BMI and body composition.

RESULTS

The mean age (range) of our cohort was 73 (65-93); 58.4% was male. Seventy-seven participants were undernourished and 21 participants had poor appetite (CNAQ < 28). A lower abundance of the genus Blautia was associated with undernutrition (log2 fold change = -0.57, Benjamini-Hochberg-adjusted P = 0.008), whereas higher abundances of taxa from Lachnospiraceae, Ruminococcaceae UCG-002, Parabacteroides merdae, and Dorea formicigenerans were associated with poor appetite. Furthermore, participants with poor appetite or undernutrition had reduced levels of faecal acetate (P = 0.006 and 0.026, respectively). Finally, there was a trend for the mice that received faecal microbiota from older adults with low BMI to weigh 1.26 g less after 3 weeks (P = 0.086) and have 6.13% more lean mass (in % body weight, P = 0.067) than the mice that received faecal microbiota from older adults without low BMI or recent weight loss.

CONCLUSIONS

This study demonstrates several associations of the gut microbiota with both poor appetite and undernutrition in older adults. Moreover, it is the first to explore a causal relation between the aged gut microbiota and body weight and body composition in the host. Possibly, microbiota-manipulating strategies will benefit older adults prone to undernutrition.

Very Preterm Children Gut Microbiota Comparison at the Neonatal Period of 1 Month and 3.5 Years of Life

Prematurity is a risk factor for dysbiosis of the gut microbiota due to particular birth conditions and frequent prolonged hospitalization of neonates. Although gut microbiota colonization after birth and its establishment during the hospitalization period have been studied in preterm infants, data on gut microbiota following discharge, particularly during early childhood, are scarce. The present study investigated the relationship between gut microbiota at 1 month after birth (hospitalization period) and 3.5 years of age in 159 preterm children belonging to the French EPIFLORE prospective observational cohort study. Analysis using bacterial 16S rRNA gene sequencing showed that the gut microbiota of preterm neonates at 1 month was highly variable and characterized by six distinct enterotypes. In contrast, the gut microbiota of the same children at 3.5 years of age showed less variability, with only two discrete enterotypes. An absence of association between enterotypes at 1 month and 3.5 years of age was observed. While the alpha diversity of gut microbiota significantly increased between 1 month and 3.5 years of age, for both alpha and beta diversities, there was no correlation between the 1-month and 3.5-years time points. Comparison at 3.5 years between children born either preterm (n = 159) or full-term (n = 200) showed no differences in terms of enterotypes, but preterm children harbored a lower Shannon diversity index and a different overall composition of microbiota than full-term children. This study suggests that the characteristics of the early gut microbiota of preterm children are not predictive of the microbial community composition at 3.5 years of age. However, the impact of gestational age is still noticeable on the gut microbiota up to 3.5 years of age.

Diet Quality and the Gut Microbiota in Women Living in Alabama

INTRODUCTION

The gut microbiota is associated with obesity and modulated by individual dietary components. However, the relationships between diet quality and the gut microbiota and their potential interactions with weight status in diverse populations are not well understood. This study examined the associations between overall diet quality, weight status, and the gut microbiota in a racially balanced sample of adult females.

METHODS

Female participants (N=71) residing in Birmingham, Alabama provided demographics, anthropometrics, biospecimens, and dietary data in this observational study from March 2014 to August 2014, and data analysis was conducted from August 2017 to March 2019. Weight status was defined as a BMI (weight [kg]/height [m²]) <30 kg/m² for non-obese participants and ≥30 kg/m² for participants who were obese. Dietary data collected included an Automated Self-Administered 24-Hour recall and Healthy Eating Index-2010 (HEI-2010) score. Diet quality was defined as having a high HEI score (≥median) or a low HEI score (<median). The fecal microbiota was collected, and the 16S ribosomal RNA gene was amplified to profile the microbiota composition. Differences in diet quality based on weight status were assessed using 2-sample t-tests. The associations between diet quality, gut microbiota, and weight status were analyzed using negative binomial models.

RESULTS

Participants (43 Black, 28 White) aged 40.39±13.86 years who were non-obese (56%) and obese (44%) were studied. Greater alpha diversity was observed among those with higher Healthy Eating Index scores (p=0.037) but did not differ by weight status. Higher abundances of Bacteroidetes (p=0.006) and Firmicutes (p=0.042) were associated with a higher HEI score. Higher Bacteriodetes levels were observed among non-obese (p=0.006).

CONCLUSIONS

Diet quality measured by the HEI was associated with alpha diversity of the gut microbiota among adult females. Abundances of phyla that have been linked with weight status (Bacteroidetes and Firmicutes) were positively associated with diet quality.

The impact of prebiotic fructooligosaccharides on gut dysbiosis and inflammation in obesity and diabetes related kidney disease

Obesity is an extensive health problem worldwide that is frequently associated with diabetes. It is a risk factor for the development of several diseases including diabetic nephropathy. Recent studies have reported that gut dysbiosis aggravates the progression of obesity and diabetes by increasing the production of uremic toxins in conjunction with gut barrier dysfunction which then leads to increased passage of lipopolysaccharides (LPS) into the blood circulatory system eventually causing systemic inflammation. Therefore, the modification of gut microbiota using a prebiotic supplement may assist in the restoration of gut barrier function and reduce any disturbance of the inflammatory response. In this review information has been compiled concerning the possible mechanisms involved in an increase in obesity, diabetes and kidney dysfunction via the exacerbation of the inflammatory response and its association with gut dysbiosis. In addition, the role of fructooligosaccharides (FOS), a source of prebiotic widely available commercially, on the improvement of gut dysbiosis and attenuation of inflammation on obese and diabetic conditions has been reviewed. The evidence confirms that FOS supplementation could improve the pathological changes associated with obesity and diabetes related kidney disease, however, knowledge concerning the mechanisms involved is still limited and needs further elucidation.

Gastrointestinal symbiont diversity in wild gorilla: a comparison of bacterial and strongylid communities across multiple localities

Western lowland gorillas (Gorilla gorilla gorilla) are Critically Endangered and show continued population decline. Consequently, pressure mounts to better understand their conservation threats and ecology. Gastrointestinal symbionts, such as bacterial and eukaryotic communities, are believed to play vital roles in the physiological landscape of the host. Gorillas host a broad spectrum of eucaryotes, so called parasites, with strongylid nematodes being particularly prevalent. While these communities are partially consistent, they are also shaped by various ecological factors, such as diet or habitat type. To investigate gastrointestinal symbionts of wild western lowland gorillas, we analysed 215 faecal samples from individuals in five distinct localities across the Congo Basin, using high-throughput sequencing techniques. We describe the gut bacterial microbiome and genetic diversity of strongylid communities, including strain-level identification of amplicon sequence variants (ASVs). We identified strongylid ASVs from eight genera and bacterial ASVs from twenty phyla. We compared these communities across localities, with reference to varying environmental factors among populations, finding differences in alpha diversity and community compositions of both gastrointestinal components. Moreover, we also investigated covariation between strongylid nematodes and the bacterial microbiome, finding correlations between strongylid taxa and Prevotellaceae and Rikenellaceae ASVs that were consistent across multiple localities. Our research highlights complexity of the bacterial microbiome and strongylid communities in several gorilla populations and emphasizes potential interactions between these two symbiont communities. This study provides a framework for ongoing research into strongylid nematode diversity, and their interactions with the bacterial microbiome, amongst great apes.

Microbiota Composition and Diversity in Weight Loss Population After the Intake of IQP-AE-103 in a Double-Blind, Randomized, Placebo-Controlled Study

The effect of the novel IQP-AE-103 (proprietary combination of dehydrated okra powder and inulin) on body weight reduction and the association with changes in microbiota composition were investigated in a double-blind, randomized, placebo-controlled trial. A total of seventy-two overweight or moderately obese subjects with a body mass index of ≥25 and <35 kg/m² were randomly allocated to receive IQP-AE-103 or placebo; each group received two IQP-AE-103 or placebo capsules three times daily, respectively. Body weight, body fat, waist circumference, and hip circumference were measured, and fecal samples were collected at baseline and after 12 weeks of intervention. Using 16S rRNA gene sequencing on the fecal samples, the microbiota dissimilarity, diversity, and differences in relative abundance between or within groups were analyzed. At the end of the study, body weight was significantly reduced in the IQP-AE-103 group compared with the placebo group, 5.16 ± 2.39 kg vs. 0.97 ± 2.09 kg (p < 0.001). Subjects from the IQP-AE-103 group who achieved a reduction of ≥5% of total body weight from baseline (hereafter referred to as 5% responders or IQP5) had a mean body weight reduction of 6.74 ± 1.94 kg, significantly greater than the placebo group (p < 0.001). Using Lefse and statistical analysis, subjects in the IQP-AE-103 group had a significantly lower relative abundance of Firmicutes than the placebo group (p < 0.05) after 12 weeks of intervention. The 5% responders from the IQP-AE-103 group had a remarkable 4.6-fold higher relative abundance of Akkermansia muciniphila than the placebo group (p < 0.05). As the significant differences between groups were only observed post-intervention, the overall differences in microbiota profile suggest that the weight loss in overweight and moderately obese subjects who consumed IQP-AE-103 for 12 weeks is accompanied by a positive change in microbiota composition. These changes might be linked to the beneficial effects of microbiome modulations in alleviating obesity and metabolic syndrome. To the best of our knowledge, we are the first to report over-the-counter (OTC) supplementation that results in both significant changes in weight and favorable shifts on the subject microbiota profile. The trial is registered under ClinicalTrials.gov Identifier no. NCT03058367.

The impacts of bovine milk, soy beverage, or almond beverage on the growing rat microbiome

Background

Milk, the first food of mammals, helps to establish a baseline gut microbiota. In humans, milk and milk products are consumed beyond infancy, providing comprehensive nutritional value. Non-dairy beverages, produced from plant, are increasingly popular as alternatives to dairy milk. The nutritive value of some plant-based products continues to be debated, whilst investigations into impacts on the microbiome are rare. The aim of this study was to compare the impact of bovine milk, soy and almond beverages on the rat gut microbiome. We previously showed soy and milk supplemented rats had similar bone density whereas the almond supplemented group had compromised bone health. There is an established link between bone health and the microbiota, leading us to hypothesise that the microbiota of groups supplemented with soy and milk would be somewhat similar, whilst almond supplementation would be different.

Methods

Three-week-old male Sprague Dawley rats were randomly assigned to five groups (n = 10/group) and fed ad libitum for four weeks. Two control groups were fed either standard diet (AIN-93G food) or AIN-93G amino acids (AA, containing amino acids equivalent to casein but with no intact protein) and with water provided ad libitum. Three treatment groups were fed AIN-93G AA and supplemented with either bovine ultra-heat treatment (UHT) milk or soy or almond UHT beverages as their sole liquid source. At trial end, DNA was extracted from caecum contents, and microbial abundance and diversity assessed using high throughput sequencing of the V3 to V4 variable regions of the 16S ribosomal RNA gene.

Results

Almost all phyla (91%) differed significantly (FDR < 0.05) in relative abundance according to treatment and there were distinct differences seen in community structure between treatment groups at this level. At family level, forty taxa showed significantly different relative abundance (FDR < 0.05). Bacteroidetes (Bacteroidaceae) and Firmicutes populations (Lactobacillaceae, Clostridiaceae and Peptostreptococcaceae) increased in relative abundance in the AA almond supplemented group. Supplementation with milk resulted in increased abundance of Actinobacteria (Coriobacteriaceae and Bifidobacteriaceae) compared with other groups. Soy supplementation increased abundance of some Firmicutes (Lactobacilliaceae) but not Actinobacteria, as previously reported by others.

Conclusion

Supplementation with milk or plant-based drinks has broad impacts on the intestinal microbiome of young rats. Changes induced by cow milk were generally in line with previous reports showing increased relative abundance of Bifidobacteriacea, whilst soy and almond beverage did not. Changes induced by soy and almond drink supplementation were in taxa commonly associated with carbohydrate utilisation. This research provides new insight into effects on the microbiome of three commercially available products marketed for similar uses.

A High-Fat Diet Induces Low-Grade Cochlear Inflammation in CD-1 Mice

There is growing evidence for a relationship between gut dysbiosis and hearing loss. Inflammatory bowel disease, diet-induced obesity (DIO), and type 2 diabetes have all been linked to hearing loss. Here, we investigated the effect of a chronic high-fat diet (HFD) on the development of inner ear inflammation using a rodent model. Three-week-old CD-1 (Swiss) mice were fed an HFD or a control diet for ten weeks. After ten weeks, mouse cochleae were harvested, and markers of cochlear inflammation were assessed at the protein level using immunohistochemistry and at the gene expression level using quantitative real-time RT-PCR. We identified increased immunoexpression of pro-inflammatory biomarkers in animals on an HFD, including intracellular adhesion molecule 1 (ICAM1), interleukin 6 receptor α (IL6Rα), and toll-like-receptor 2 (TLR2). In addition, increased numbers of ionized calcium-binding adapter molecule 1 (Iba1) positive macrophages were found in the cochlear lateral wall in mice on an HFD. In contrast, gene expression levels of inflammatory markers were not affected by an HFD. The recruitment of macrophages to the cochlea and increased immunoexpression of inflammatory markers in mice fed an HFD provide direct evidence for the association between HFD and cochlear inflammation.

Characteristics of the gut microbiota in pregnant women with fetal growth restriction

Background

Fetal growth restriction (FGR) in utero leads to failure of fetus to reach the genetically normal growth potential. Currently available means of treating FGR are limited. And it remains unknown how pregnant women who give birth to FGR fetus differ in gut microbiota composition from normal pregnant women.

Methods

In this case-control study, fecal samples were obtained from maternal rectum in the operation room by an obstetrician under strict aseptic conditions. We compared gut microbiota of 14 pregnant women with FGR and 18 normal controls by performing 16S rDNA amplicon sequencing.

Results

We identified significant differences in β-diversity between the FGR and control groups (P < 0.05). At genus level, Bacteroides, Faecalibacterium and Lachnospira were highly abundant in the FGR subjects, which are significantly enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to glycometabolism.

Conclusion

These findings demonstrated that the distinct composition of the gut microbiota between FGR and normal pregnant women could contribute to an improved understanding of the prevention and treatment of FGR.

Effects of caloric restriction on the gut microbiome are linked with immune senescence

BACKGROUND

Caloric restriction can delay the development of metabolic diseases ranging from insulin resistance to type 2 diabetes and is linked to both changes in the composition and metabolic function of the gut microbiota and immunological consequences. However, the interaction between dietary intake, the microbiome, and the immune system remains poorly described.

RESULTS

We transplanted the gut microbiota from an obese female before (AdLib) and after (CalRes) an 8-week very-low-calorie diet (800 kcal/day) into germ-free mice. We used 16S rRNA sequencing to evaluate taxa with differential abundance between the AdLib- and CalRes-microbiota recipients and single-cell multidimensional mass cytometry to define immune signatures in murine colon, liver, and spleen. Recipients of the CalRes sample exhibited overall higher alpha diversity and restructuring of the gut microbiota with decreased abundance of several microbial taxa (e.g., Clostridium ramosum, Hungatella hathewayi, Alistipi obesi). Transplantation of CalRes-microbiota into mice decreased their body fat accumulation and improved glucose tolerance compared to AdLib-microbiota recipients. Finally, the CalRes-associated microbiota reduced the levels of intestinal effector memory CD8+ T cells, intestinal memory B cells, and hepatic effector memory CD4+ and CD8+ T cells.

CONCLUSION

Caloric restriction shapes the gut microbiome which can improve metabolic health and may induce a shift towards the naïve T and B cell compartment and, thus, delay immune senescence. Understanding the role of the gut microbiome as mediator of beneficial effects of low calorie diets on inflammation and metabolism may enhance the development of new therapeutic treatment options for metabolic diseases.

TRIAL REGISTRATION

NCT01105143 , "Effects of negative energy balance on muscle mass regulation," registered 16 April 2010. Video Abstract.

Ulva prolifera polysaccharide exerts anti-obesity effects via upregulation of adiponectin expression and gut microbiota modulation in high-fat diet-fed C57BL/6 mice

Obesity is characterized by metabolic disorder and accompanying an altered and less diverse gut microbiota composition during a fat-enriched diet. Recent studies indicated that sulphated polysaccharide prevents high-fat diet (HFD) induced obesity, reduces metabolic disorder, and restores the gut microbiota. However, there are few studies about Ulva prolifera polysaccharide (UPP) may induce anti-obesogenic effects. Therefore, the present study investigates the enzymatic extracted UPP effects in HFD-fed mice. The results showed that UPP considerably slowed down the HFD-induced weight gain and improved metabolic disorders in HFD-fed mice. Notably, the effects were associated with lower body weight gain, reduced adipose tissue hypertrophy, triglyceride concentration in liver and systemic low-grade inflammation, and improved fasting blood glucose. Moreover, our result reveals that UPP may elevate the expression of AMPK via adiponectin activation. Interestingly, we found that UPP may induce PPARα agonist to enhance β-oxidation since the elevation of CPT-1 and PPARα expression simultaneously. Meanwhile, gut microbiota analysis revealed UPP promoted the growth of Parasutterella, Feacalibaculum, and Bifidobacterium, and reduced the abundance of Acetatifactor, Tyzerella, Ruminococcus_1, and Desulfovibrio. The changes in microbiota may have a positively correlated effect on improving obesity and metabolic abnormalities. UPP may prevent HFD-induced obesity and associated metabolic diseases, as well as modulate the composition of gut microbiota to facilitate the growth of probiotics.

Chronic Embryo-Larval Exposure of Fathead Minnows to the Pharmaceutical Drug Metformin: Survival, Growth, and Microbiome Responses

Metformin is a glucose-lowering drug commonly found in municipal wastewater effluents (MWWEs). The present study investigated the chronic effects of metformin in early-life stages of the fathead minnow (Pimephales promelas). Endpoints assessed were growth, survival, and deformities. The larval gut microbiome was also examined using 16 S ribosomal RNA gene amplicon sequencing to determine microbial community composition and alpha and beta diversity. Eggs and larvae were exposed to metformin measured concentrations (mean [standard deviation]) of 0.020 (0.017) μg/L (for controls) and 3.44 (0.23), 33.6 (1.6), and 269 (11) μg/L in a daily static-renewal setup, with 20 embryos per beaker. The low and middle metformin exposure concentrations represent river and MWWE concentrations of metformin. To detect small changes in growth, we used 18 replicate beakers for controls and 9 replicates for each metformin treatment. Over the 21-d exposure (5 d as embryos and 16 d posthatch [dph]), metformin did not affect survival or growth of larval fish. Hatch success, time to hatch, deformities in hatched fry, and survival were similar across all treatments. Growth (wet wt, length, and condition factor) assessed at 9 and 16 dph was also unaffected by metformin. Assessment of the microbiome showed that the larvae microbiome was dominant in Proteobacteria and Firmicutes, with small increases in Proteobacteria and decreases in Firmicutes with increasing exposure to metformin. No treatment effects were found for microbiome diversity measures. Control fish euthanized with the anesthetic tricaine methane sulfonate had decreased alpha diversity compared to those sampled by spinal severance. This experiment demonstrates that metformin at environmentally relevant concentrations (3.44 and 33.6 μg/L) and at 10 times MWWE concentrations (269 µg/L) does not adversely affect larval growth or gut microbiome in this ubiquitous freshwater fish species. Environ Toxicol Chem 2022;41:635-647. © 2021 Her Majesty the Queen in Right of Canada. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada.

Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest

Gut microbiota play a significant role for animals to adapt to the changing environment. Host species and habitats are key drivers in shaping the diversity and composition of the microbiota, but the determinants of composition of the sympatric host gut microbiome remain poorly understood within an ecosystem. In this study, we examined the effects of habitats of different succession stages and host species on the diversity and composition of fecal gut microbiota in four sympatric rodent species (Apodemus draco, Leopoldamys edwardsi, Niviventer confucianus, and Niviventer fulvescens) in a subtropical forest. We found, as compared to the differences between species, habitat types showed a much larger effect on the gut microbiota of rodents. Alpha diversity of the microbial community of A. draco, N. fulvescens, and N. confucianus was highest in farmland, followed by primary forest and shrubland, and lowest in secondary forest. Beta diversity of the three rodent species showed significant different among habitats. The alpha diversity of gut microbiota of L. edwardsi was significantly higher than those of A. draco and N. confucianus, and its beta diversity showed significant difference from A. draco. Our results suggested that gut microbiota were important for animals in responding to diet changes in different habitats under human disturbances.

Gut microbiota in patients with obesity and metabolic disorders - a systematic review

BACKGROUND

Previous observational studies have demonstrated inconsistent and inconclusive results of changes in the intestinal microbiota in patients with obesity and metabolic disorders. We performed a systematic review to explore evidence for this association across different geography and populations.

METHODS

We performed a systematic search of MEDLINE (OvidSP) and Embase (OvidSP) of articles published from Sept 1, 2010, to July 10, 2021, for case-control studies comparing intestinal microbiome of individuals with obesity and metabolic disorders with the microbiome of non-obese, metabolically healthy individuals (controls). The primary outcome was bacterial taxonomic changes in patients with obesity and metabolic disorders as compared to controls. Taxa were defined as "lean-associated" if they were depleted in patients with obesity and metabolic disorders or negatively associated with abnormal metabolic parameters. Taxa were defined as "obesity-associated" if they were enriched in patients with obesity and metabolic disorders or positively associated with abnormal metabolic parameters.

RESULTS

Among 2390 reports screened, we identified 110 full-text articles and 60 studies were included. Proteobacteria was the most consistently reported obesity-associated phylum. Thirteen, nine, and ten studies, respectively, reported Faecalibacterium, Akkermansia, and Alistipes as lean-associated genera. Prevotella and Ruminococcus were obesity-associated genera in studies from the West but lean-associated in the East. Roseburia and Bifidobacterium were lean-associated genera only in the East, whereas Lactobacillus was an obesity-associated genus in the West.

CONCLUSIONS

We identified specific bacteria associated with obesity and metabolic disorders in western and eastern populations. Mechanistic studies are required to determine whether these microbes are a cause or product of obesity and metabolic disorders.

Tipping the Balance: Vitamin D Inadequacy in Children Impacts the Major Gut Bacterial Phyla

Vitamin D inadequacy appears to be on the rise globally, and it has been linked to an increased risk of osteoporosis, as well as metabolic, cardiovascular, and autoimmune diseases. Vitamin D concentrations are partially determined by genetic factors. Specific single nucleotide polymorphisms (SNPs) in genes involved in vitamin D transport, metabolism, or binding have been found to be associated with its serum concentration, and these SNPs differ among ethnicities. Vitamin D has also been suggested to be a regulator of the gut microbiota and vitamin D deficiency as the possible cause of gut microbial dysbiosis and inflammation. This pilot study aims to fill the gap in our understanding of the prevalence, cause, and implications of vitamin D inadequacy in a pediatric population residing in Qatar. Blood and fecal samples were collected from healthy subjects aged 4–14 years. Blood was used to measure serum metabolite of vitamin D, 25-hydroxycholecalciferol 25(OH)D. To evaluate the composition of the gut microbiota, fecal samples were subjected to 16S rRNA gene sequencing. High levels of vitamin D deficiency/insufficiency were observed in our cohort with 97% of the subjects falling into the inadequate category (with serum 25(OH)D < 75 nmol/L). The CT genotype in rs12512631, an SNP in the GC gene, was associated with low serum levels of vitamin D (ANOVA, p = 0.0356) and was abundant in deficient compared to non-deficient subjects. Overall gut microbial community structure was significantly different between the deficient (D) and non-deficient (ND) groups (Bray Curtis dissimilarity p = 0.049), with deficient subjects also displaying reduced gut microbial diversity. Significant differences were observed among the two major gut phyla, Firmicutes (F) and Bacteroidetes (B), where deficient subjects displayed a higher B/F ratio (p = 0.0097) compared to ND. Vitamin D deficient children also demonstrated gut enterotypes dominated by the genus Prevotella as opposed to Bacteroides. Our findings suggest that pediatric vitamin D inadequacy significantly impacts the gut microbiota. We also highlight the importance of considering host genetics and baseline gut microbiome composition in interpreting the clinical outcomes related to vitamin D deficiency as well as designing better personalized strategies for therapeutic interventions.

The Mediating Role of the Gut Microbiota in the Physical Growth of Children

Gut microbiota succession overlaps with intensive growth in infancy and early childhood. The multitude of functions performed by intestinal microbes, including participation in metabolic, hormonal, and immune pathways, makes the gut bacterial community an important player in cross-talk between intestinal processes and growth. Long-term disturbances in the colonization pattern may affect the growth trajectory, resulting in stunting or wasting. In this review, we summarize the evidence on the mediating role of gut microbiota in the mechanisms controlling the growth of children.

Roles of gut microbiota and metabolites in overweight and obesity of children

The prevalence of overweight and obesity in children and adolescents is an increasing public health problem. Pediatric overweight and obesity result from multiple factors, including genetic background, diet, and lifestyle. In addition, the gut microbiota and their metabolites play crucial roles in the progression of overweight and obesity of children. Therefore, we reviewed the roles of gut microbiota in overweight/obese children. The relationship between pediatric overweight/obesity and gut metabolites, such as short-chain fatty acids, medium-chain fatty acids, amino acids, amines, and bile acids, are also summarized. Targeting gut microbiota and metabolites might be a promising strategy for interventions aimed at reducing pediatric overweight/obesity.

Vitamin B-12 and the Gastrointestinal Microbiome: A Systematic Review

Vitamin B-12 deficiency is a major public health problem affecting individuals across the lifespan, with known hematological, neurological, and obstetric consequences. Emerging evidence suggests that vitamin B-12 may have an important role in other aspects of human health, including the composition and function of the gastrointestinal (gut) microbiome. Vitamin B-12 is synthesized and utilized by bacteria in the human gut microbiome and is required for over a dozen enzymes in bacteria, compared to only two in humans. However, the impact of vitamin B-12 on the gut microbiome has not been established. This systematic review was conducted to examine the evidence that links vitamin B-12 and the gut microbiome. A structured search strategy was used to identify in vitro, animal, and human studies that assessed vitamin B-12 status, dietary intake, or supplementation, and the gut microbiome using culture-independent techniques. A total of 22 studies (3 in vitro, 8 animal, 11 human observational studies) were included. Nineteen studies reported vitamin B-12 intake, status, or supplementation was associated with gut microbiome outcomes, including beta-diversity, alpha-diversity, relative abundance of bacteria, functional capacity, or short chain fatty acid production. Evidence suggests vitamin B-12 may be associated with changes in bacterial abundance. While results from in vitro studies suggest vitamin B-12 may increase alpha-diversity and shift gut microbiome composition (beta-diversity), findings from animal studies and observational human studies were heterogeneous. Based on evidence from in vitro and animal studies, microbiome outcomes may differ by cobalamin form and co-intervention. To date, few prospective observational studies and no randomized trials have been conducted to examine the effects of vitamin B-12 on the human gut microbiome. The impact of vitamin B-12 on the gut microbiome needs to be elucidated to inform screening and public health interventions. Statement of significance: Vitamin B-12 is synthesized and utilized by bacteria in the human gut microbiome and is required by over a dozen enzymes in bacteria. However, to date, no systematic reviews have been conducted to evaluate the impact of vitamin B-12 on the gut microbiome, or its implications for human health.

Fecal bacterial communities of wild black capuchin monkeys (Sapajus nigritus) from the Atlantic Forest biome in Southern Brazil are divergent from those of other non-human primates

Gut microbiota are influenced by factors such as diet, habitat, and social contact, which directly affect the host's health. Studies related to gut microbiota in non-human primates are increasing worldwide. However, little remains known about the gut bacterial composition in wild Brazilian monkeys. Therefore, we studied the fecal microbiota composition of wild black capuchin monkey (Sapajus nigritus) (n=10) populations from two different Atlantic Forest biome fragments (five individuals per fragment) in south Brazil. The bacterial community was identified via the high-throughput sequencing and partial amplification of the 16S rRNA gene (V4 region) using an Ion Personal Genome Machine (PGMTM) System. In contrast to other studies involving monkey microbiota, which have generally reported the phyla Firmicutes and Bacteroidetes as predominant, black capuchin monkeys showed a high relative abundance of Proteobacteria ( χ ¯ = 80.54%), followed by Firmicutes ( χ ¯ = 12.14%), Actinobacteria ( χ ¯ = 4.60%), and Bacteriodetes ( χ ¯ = 1.31%). This observed particularity may have been influenced by anthropogenic actions related to the wild habitat and/or diet specific to the Brazilian biome's characteristics and/or monkey foraging behavior. Comparisons of species richness (Chao1) and diversity indices (Simpson and InvSimpson) showed no significant differences between the two groups of monkeys. Interestingly, PICRUSt2 analysis revealed that metabolic pathways present in the bacterial communities were associated with xenobiotic biodegradation and the biosynthesis of secondary metabolites, which may suggest positive effects on monkey health and conservation in this anthropogenic habitat. Infectious disease-associated microorganisms were also observed in the samples. The present study provides information about the bacterial population and metabolic functions present in fecal microbiota, which may contribute to a better understanding of the ecology and biology of black capuchin monkeys living in forest fragments within the Atlantic Forest biome in southern Brazil. Additionally, the present study demonstrates that the fecal bacterial communities of wild black capuchin monkeys in this area are divergent from those of other wild non-human primates.

Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut

Supplementation with micronutrients, including vitamins, iron and zinc, is a key strategy to alleviate child malnutrition. However, association of gastrointestinal disorders with iron has led to ongoing debate over their administration. To better understand their impact on gut microbiota, we analyse the bacterial, protozoal, fungal and helminth communities of stool samples collected from a subset of 80 children at 12 and 24 months of age, previously enrolled into a large cluster randomized controlled trial of micronutrient supplementation in Pakistan (ClinicalTrials.gov identifier NCT00705445). We show that while bacterial diversity is reduced in supplemented children, vitamins and iron (as well as residence in a rural setting) may promote colonization with distinct protozoa and mucormycetes, whereas the addition of zinc appears to ameliorate this effect. We suggest that the risks and benefits of micronutrient interventions may depend on eukaryotic communities, potentially exacerbated by exposure to a rural setting. Larger studies are needed to evaluate the clinical significance of these findings and their impact on health outcomes.

Assessment of the Effects of Dietary Vitamin D Levels on Olanzapine-Induced Metabolic Side Effects: Focus on the Endocannabinoidome-Gut Microbiome Axis

Vitamin D deficiency is associated with poor mental health and dysmetabolism. Several metabolic abnormalities are associated with psychotic diseases, which can be compounded by atypical antipsychotics that induce weight gain and insulin resistance. These side-effects may be affected by vitamin D levels. The gut microbiota and endocannabinoidome (eCBome) are significant regulators of both metabolism and mental health, but their role in the development of atypical antipsychotic drug metabolic side-effects and their interaction with vitamin D status is unknown. We studied the effects of different combinations of vitamin D levels and atypical antipsychotic drug (olanzapine) exposure on whole-body metabolism and the eCBome-gut microbiota axis in female C57BL/6J mice under a high fat/high sucrose (HFHS) diet in an attempt to identify a link between the latter and the different metabolic outputs induced by the treatments. Olanzapine exerted a protective effect against diet-induced obesity and insulin resistance, largely independent of dietary vitamin D status. These changes were concomitant with olanzapine-mediated decreases in Trpv1 expression and increases in the levels of its agonists, including various N-acylethanolamines and 2-monoacylglycerols, which are consistent with the observed improvement in adiposity and metabolic status. Furthermore, while global gut bacteria community architecture was not altered by olanzapine, we identified changes in the relative abundances of various commensal bacterial families. Taken together, changes of eCBome and gut microbiota families under our experimental conditions might contribute to olanzapine and vitamin D-mediated inhibition of weight gain in mice on a HFHS diet.

Epigallocatechin Gallate (EGCG) Promotes the Immune Function of Ileum in High Fat Diet Fed Mice by Regulating Gut Microbiome Profiling and Immunoglobulin Production

This study aimed to investigate the regulatory effect of epigallocatechin gallate (EGCG) on the composition of the gut microbiome, the transcriptomic profiling of ileum, and their interplay in high fat diet (HFD) induced obese mice. Intragastric administration of EGCG to C57BL/6J mice for 14 consecutive weeks remarkably decreased HFD induced excessive fat deposition (p < 0.001), and the increment of serum TG, TC, HDL-C (p < 0.05), as well as improved glucose tolerance (p < 0.001). EGCG shifted the gut microbiota mainly by elevating the relative abundance of Parasutterrlla, Bacteroides, and Akkermansia (p < 0.01), decreasing that of norank_f_Erysipelotrichaceae, unclassified_f_Ruminococcaceae, Anaerotruncus, Roseburia, norank_Lachnospiraceae, and Lachnospiraceae_UCG_006 (p < 0.01) at the genus level. In addition, EGCG affected the transcriptomic profiling of ileum, and the differentially expressed (DE) genes after HFD or/and EGCG treatment were mostly enriched in the immune reaction of ileum, such as the GO term of “immune effector process” and “phagocytosis, recognition.” Furthermore, the KEGG category of “immune diseases,” “immune system,” and “infection diseases: bacterial” were commonly enriched by the DE genes of the two treatments. Among those DE genes, 16 immunoglobulins heavy chain variable region encoded genes (Ighvs) and other immunity-related genes, such as complement component 2 (C2), interferon-induced transmembrane protein 1 (Iftm1), polymeric immunoglobulin receptor (pigR), and alanyl aminopeptidase (Anpep), were highly correlated with the shifted microbes in the gut (p < 0.05, absolute r > 0.5). Overall, the results suggested that EGCG ameliorated the HFD induced metabolic disorder mainly by regulating gut microbiome profiling and the immunoglobulin production of ileum, while the genes expressed in the ileum, especially Ighvs, C2, Iftm1, pigR, and Anpep, might play important roles in coordinating the immunity of mice regarding the gut microbes and the host interactions.

In vitro fecal fermentation profiles and microbiota responses of pulse cell wall polysaccharides: enterotype effect

The gut microbiota community of individuals is predominated by diverse fiber-utilizing bacteria, and might have distinct fermentation outcomes for a given dietary substrate. In this research, we isolated pea cell walls (PCWs) from cotyledon seeds, and performed the in vitro fecal fermentation by individual Prevotella- and Bacteroides-enterotype inocula. The Prevotella-enterotype inoculum showed a higher fermentation rate and produced more short-chain fatty acids (SCFAs), especially propionate and butyrate, throughout the entire fermentation period from PCW degradation compared with the Bacteroides-enterotype one. Furthermore, the better monosaccharide utilization capacity of Prevotella-enterotype inoculum was shown, compared to the Bacteroides-enterotype inoculum. PCW fermentation with Prevotella- and Bacteroides-enterotype inocula resulted in different microbial changes, and the abundance of Prevotella and Bacteroides was promoted, respectively. These results may contribute to predicting the responses of Prevotella and Bacteroides enterotypes to diets and offer useful information in personalized nutrition.

Effect of Lycium barbarum polysaccharide supplementation in non-alcoholic fatty liver disease patients: study protocol for a randomized controlled trial

Background

Non-alcohol fatty liver disease (NAFLD) is the most common chronic liver disease in the world, with a high incidence and no effective treatment. At present, the targeted therapy of intestinal microbes for NAFLD is highly valued. Lycium barbarum polysaccharide (LBP), as the main active ingredient of Lycium barbarum, is considered to be a new type of prebiotic substance, which can improve NAFLD by regulating the gut microbiota. The purpose of this study is to evaluate the safety and efficacy of LBP supplementation in modulating gut microbiota for NAFLD patients.

Methods

This randomized, double-blind, placebo-control study will be conducted in the physical examination center of the Ningxia Hui Autonomous Region People’s Hospital. A total of 50 patients with NAFLD confirmed by abdominal ultrasound, laboratory tests, and questionnaire surveys will be recruited and randomly assigned into the control group (maltodextrin placebo capsules) and the intervention group (LBP supplementation capsules) for 3 months. Neither patients, nor investigators, nor data collectors will know the contents in each capsule and the randomization list. The primary outcome measure is the level of ALT concentration relief after the intervention. Secondary outcomes include gut microbiota abundance and diversity, intestinal permeability, patient’s characteristic demographic data and body composition, adverse effects, and compliance from patients.

Discussion

LBPs are potential prebiotics with the property of regulating host gut microbiota. Our previous studies have documented that LBP supplement can improve the liver damage and the gut microflora dysbiosis in NAFLD rats. This treatment would provide a more in-depth understanding of the effect of this LBP supplementation.

Trial registration

Chinese Clinical Trial Register, ChiCTR2000034740. Registered on 17 July 2020.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-021-05529-6.

Altered Microbial Composition of Drug-Sensitive and Drug-Resistant TB Patients Compared with Healthy Volunteers

Mycobacterium tuberculosis infection has three discernible outcomes: active tuberculosis, latent tuberculosis, or clearance of the bacterium. The outcome of the infection depends on the interaction of the bacterium, the immune system, and the microbiome of the host. The current study uses 16S rRNA sequencing to determine the diversity and composition of the respiratory microbiome of drug-resistant and drug-sensitive tuberculosis patients as well as healthy volunteers. Tuberculosis patients exhibited increased microbial diversity and differentially abundant bacteria than healthy volunteers. Compositional differences were also observed when comparing drug-sensitive or -resistant tuberculosis patients. Finally, we defined and assessed the differences in the core sputum microbiota between tuberculosis patients and healthy volunteers. Our observations collectively suggest that in sputum, Mycobacterium tuberculosis infection is related to altered bacterial diversity and compositional differences of core members of the microbiome, with potential implications for the bacterial pulmonary ecosystem's stability and function.