The Gut Microbiome and Obesity

Prevalence of Blastocystis and its association with Firmicutes/Bacteroidetes ratio in clinically healthy and metabolically ill subjects

BACKGROUND

Blastocystis is a typical anaerobic colon protist in humans with controversial pathogenicity and has relation with alterations in the intestinal microbiota composition (dysbiosis), whose eventual indicator is the Firmicutes/Bacteroidetes ratio (F/B ratio); this indicator is also linked to complications such as diabetes, obesity, or inflammatory bowel disease. The present study investigated the prevalence of Blastocystis and its association with Firmicutes/Bacteroidetes ratio in healthy and metabolic diseased subjects.

METHODS

Fecal and blood samples were collected consecutively from 200 healthy subjects and 84 subjects with metabolic disease; Blastocystis and its most frequent subtypes were identified by end-point PCR and the two most representative phyla of the intestinal microbiota Firmicutes and Bacteroidetes by real-time PCR.

RESULTS

The prevalence of Blastocystis in healthy subjects was 47.0, and 65.48% in subjects with metabolic disease; the most prevalent subtype in the total population was ST3 (28.38%), followed by ST1 (14.86%), ST4, ST5, and ST7 (each one of them with 14.19% respectively), and finally ST2 (8.78%). The low F/B ratio was associated with the prevalence of Blastocystis in the two cohorts FACSA (OR = 3.78 p < 0.05) and UNEME (OR = 4.29 p < 0.05). Regarding the subtype level, an association between the FACSA cohort ST1 and ST7 with low Firmicutes/Bacteroidetes ratio was found (OR = 3.99 and 5.44 p < 0.05, respectively).

CONCLUSIONS

The evident predatory role of Blastocystis over Firmicutes phylum was observed in both cohorts since the abundance of bacterial group's Bacteroidetes increases in the groups colonized by this eukaryote and, therefore, may have a beneficial effect.

Gut Microbiome Diversity and Composition Are Associated with Habitual Dairy Intakes: A Cross-Sectional Study in Men

BACKGROUND

At a population level, the relation between dairy consumption and gut microbiome composition is poorly understood.

OBJECTIVES

We sought to study the cross-sectional associations between individual dairy foods (i.e., milk, yogurt, and cheese), as well as total dairy intake, and the gut microbiome composition in a large, representative sample of men living in south-eastern Australia.

METHODS

Data on 474 men (mean ± SD: 64.5 ± 13.5 y old) from the Geelong Osteoporosis Study were used to assess the cross-sectional association between dairy consumption and gut microbiome. Information on dairy intake was self-reported. Men were categorized as consumers and nonconsumers of milk, yogurt, cheese, and high- and low-fat milk. Milk, yogurt, and cheese intakes were summed to calculate the total dairy consumed per day and categorized into either low (<2.5 servings/d) or high (≥2.5 servings/d) total dairy groups. Fecal samples were analyzed using bacterial 16S ribosomal RNA (rRNA) gene sequencing. After assessment of α and β diversity, differential abundance analysis was performed to identify bacterial taxa associated with each of milk, yogurt, and cheese consumption compared with nonconsumption, low compared with high total dairy, and low- compared with high-fat milk consumption. All analyses were adjusted for potential confounders.

RESULTS

α Diversity was not associated with consumption of any of the dairy groups. Differences in β diversity were observed between milk and yogurt consumption compared with nonconsumption. Taxa belonging to the genera Ruminococcaceae UCG-010 and Bifidobacterium showed negative and weak positive associations with milk consumption, respectively. A taxon from the genus Streptococcus was positively associated with yogurt consumption, whereas a taxon from the genus Eisenbergiella was negatively associated with cheese consumption. No specific taxa were associated with low- compared with high-fat milk nor low compared with high total dairy consumption.

CONCLUSIONS

In men, community-level microbiome differences were observed between consumers and nonconsumers of milk and yogurt. Bacterial taxon-level associations were detected with milk, yogurt, and cheese consumption. Total dairy consumption was not associated with any microbiome measures, suggesting that individual dairy foods may have differential roles in shaping the gut microbiome in men.

Machine learning-based investigation of the relationship between gut microbiome and obesity status

Gut microbiota is believed to play a crucial role in obesity. However, the consistent findings among published studies regarding microbiome-obesity interaction are relatively rare, and one of the underlying causes could be the limited sample size of cohort studies. In order to identify gut microbiota changes between normal-weight individuals and obese individuals, fecal samples along with phenotype information from 2262 Chinese individuals were collected and analyzed. Compared with normal-weight individuals, the obese individuals exhibit lower diversity of species and higher diversity of metabolic pathways. In addition, various machine learning models were employed to quantify the relationship between obesity status and Body mass index (BMI) values, of which support vector machine model achieves best performance with 0.716 classification accuracy and 0.485 R² score. In addition to two well-established obesity-associated species, three species that have potential to be obesity-related biomarkers, including Bacteroides caccae, Odoribacter splanchnicus and Roseburia hominis were identified. Further analyses of functional pathways also reveal some enriched pathways in obese individuals. Collectively, our data demonstrates tight relationship between obesity and gut microbiota in a large-scale Chinese population. These findings may provide potential targets for the prevention and treatment of obesity.

Obesity Modulates the Gut Microbiome in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive, molecularly heterogeneous subtype of breast cancer. Obesity is associated with increased incidence and worse prognosis in TNBC through various potential mechanisms. Recent evidence suggests that the gut microbiome plays a central role in the progression of cancer, and that imbalances or dysbiosis in the population of commensal microbiota can lead to inflammation and contribute to tumor progression. Obesity is characterized by low-grade inflammation, and gut dysbiosis is associated with obesity, chronic inflammation, and failure of cancer immunotherapy. However, the debate on what constitutes a "healthy" gut microbiome is ongoing, and the connection among the gut microbiome, obesity, and TNBC has not yet been addressed. This study aims to characterize the role of obesity in modulating the gut microbiome in a syngeneic mouse model of TNBC. 16S rRNA sequencing and metagenomic analyses were performed to analyze and annotate genus and taxonomic profiles. Our results suggest that obesity decreases alpha diversity in the gut microbiome. Metagenomic analysis revealed that obesity was the only significant factor explaining the similarity of the bacterial communities according to their taxonomic profiles. In contrast to the analysis of taxonomic profiles, the analysis of variation of functional profiles suggested that obesity status, tumor presence, and the obesity-tumor interaction were significant in explaining the variation of profiles, with obesity having the strongest correlation. The presence of tumor modified the profiles to a greater extent in obese than in lean animals. Further research is warranted to understand the impact of the gut microbiome on TNBC progression and immunotherapy.

Probiotics Regulate Gut Microbiota: An Effective Method to Improve Immunity

Probiotics are beneficial active microorganisms that colonize the human intestines and change the composition of the flora in particular parts of the host. Recently, the use of probiotics to regulate intestinal flora to improve host immunity has received widespread attention. Recent evidence has shown that probiotics play significant roles in gut microbiota composition, which can inhibit the colonization of pathogenic bacteria in the intestine, help the host build a healthy intestinal mucosa protective layer, and enhance the host immune system. Based on the close relationship between the gut microbiota and human immunity, it has become an extremely effective way to improve human immunity by regulating the gut microbiome with probiotics. In this review, we discussed the influence of probiotics on the gut microbiota and human immunity, and the relationship between immunity, probiotics, gut microbiota, and life quality. We further emphasized the regulation of gut microflora through probiotics, thereby enhancing human immunity and improving people’s lives.

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon)

Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.

Modulation of gut microbiota by chondroitin sulfate calcium complex during alleviation of osteoporosis in ovariectomized rats

Although chondroitin sulfate calcium complex (CSCa) was claimed to have the bioactivity for bone care in vitro, its anti-osteoporosis bioactivity was little reported in vivo. Here, the effects of CSCa on osteoporosis rats were investigated. Results showed that, compared with the osteoporosis rats, CSCa could improve the bone mineral density and microstructure of femur, and change the bone turnover markers level in serum. 16S rRNA sequencing and metabolomics analysis indicated CSCa intervention altered the composition of gut microbiota along with metabolite profiles in ovariectomized rat faeces. The correlation analysis showed some gut microbiota taxa were significantly correlated with osteoporosis phenotypes and the enriched metabolites. Taken together, dietary CSCa intervention has the potential to alleviate the osteoporosis and related symptoms probably involving gut microbiota or the metabolite profiles as demonstrated in rats. This study provides some scientific evidence for the potential effects of CSCa as the food supplement on the osteoporosis.

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels

Background

Thirteen-lined ground squirrels (Ictidomys tridecemlineatus) are obligate hibernators and are only active 4–5 months annually. During this period, squirrels rapidly acquire fat for use during hibernation. We investigated how the gut microbiome changed over the active season in the mucosa and lumen of two gut sections: the cecum and ileum. We sequenced the 16S rRNA gene to assess diversity and composition of the squirrel gut microbiome and used differential abundance and network analyses to identify relationships among gut sections.

Results

Microbial composition significantly differed between the cecum and ileum, and within the ileum between the mucosa and lumen. Cecum mucosa and lumen samples did not differ in alpha diversity and composition, and clustered by individual squirrel. Ileum mucosa and lumen samples differed in community composition, which can likely be attributed to the transient nature of food-associated bacteria in the lumen. We did not detect a shift in microbiome diversity and overall composition over the duration of the active season, indicating that the squirrel microbiome may be relatively robust to changes in physiology.

Conclusions

Overall, we found that the 13-lined ground squirrel microbiome is shaped by microenvironment during the active season. Our results provide baseline data for new avenues of research, such as investigating potential differences in microbial function among these physiologically unique gut environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00117-0.

The Role of Gut Microbial β-Glucuronidase in Estrogen Reactivation and Breast Cancer

Over the past decade, the gut microbiota has received considerable attention for its interactions with the host. Microbial β-glucuronidase generated by this community has hence aroused concern for its biotransformation activity to a wide range of exogenous (foreign) and endogenous compounds. Lately, the role of gut microbial β-glucuronidase in the pathogenesis of breast cancer has been proposed for its estrogen reactivation activity. This is plausible considering that estrogen glucuronides are the primary products of estrogens' hepatic phase II metabolism and are subject to β-glucuronidase-catalyzed hydrolysis in the gut via bile excretion. However, research in this field is still at its very preliminary stage. This review outlines the biology of microbial β-glucuronidase in the gastrointestinal tract and elaborates on the clues to the existence of microbial β-glucuronidase-estrogen metabolism-breast cancer axis. The research gaps in this field will be discussed and possible strategies to address these challenges are suggested.

The Novel Interplay between Commensal Gut Bacteria and Metabolites in Diet-Induced Hyperlipidemic Rats Treated with Simvastatin

Hyperlipidemia is one kind of metabolic syndrome for which the treatment commonly includes simvastatin (SV). Individuals vary widely in statin responses, and growing evidence implicates gut microbiome involvement in this variability. However, the associated molecular mechanisms between metabolic improvement and microbiota composition following SV treatment are still not fully understood. In this study, combinatory approaches using ultrahigh-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF MS/MS)-based metabolomic profiling, PCR-denaturing gradient gel electrophoresis (PCR-DGGE), quantitative PCR (qPCR), and 16S rRNA gene sequencing-based gut microbiota profiling were performed to investigate the interplay of endogenous metabolites and the gut microbiota related to SV treatment. A total of 6 key differential endogenous metabolites were identified that affect the metabolism of amino acids (phenylalanine and tyrosine), unsaturated fatty acids (linoleic acid and 9-hydroxyoctadecadienoic acid (9-HODE)), and the functions of gut microbial metabolism. Moreover, a total of 22 differentially abundant taxa were obtained following SV treatment. Three bacterial taxa were identified to be involved in SV treatment, namely, Bacteroidaceae, Prevotellaceae, and Porphyromonadaceae. These findings suggested that the phenylalanine and tyrosine-associated amino acid metabolism pathways, as well as the linoleic acid and 9-HODE-associated unsaturated fatty acid metabolism pathways, which are involved in gut flora interactions, might be potential therapeutic targets for improvement in SV hypolipidemic efficacy. The mass spectrometric data have been deposited to MassIVE (https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp). Username: MSV000087842_reviewer. Password: hardworkingzsr.

Association between metabolic status and gut microbiome in obese populations

Despite that obesity is associated with many metabolic diseases, a significant proportion (10–30 %) of obese individuals is recognized as ‘metabolically healthy obeses’ (MHOs). The aim of the current study is to characterize the gut microbiome for MHOs as compared to ‘metabolically unhealthy obeses’ (MUOs). We compared the gut microbiome of 172 MHO and 138 MUO individuals from Chongqing (China) (inclined to eat red meat and food with a spicy taste), and performed validation with selected biomarkers in 40 MHOs and 33 MUOs from Quanzhou (China) (inclined to eat seafood and food with a light/bland taste). The genera Alistipes, Faecalibacterium and Odoribacter had increased abundance in both Chongqing and Quanzhou MHOs. We also observed different microbial functions in MUOs compared to MHOs, including an increased abundance of genes associated with glycan biosynthesis and metabolism. In addition, the microbial gene markers identified from the Chongqing cohort bear a moderate accuracy [AUC (area under the operating characteristic curve)=0.69] for classifying MHOs distinct from MUOs in the Quanzhou cohort. These findings indicate that gut microbiome is significantly distinct between MHOs and MUOs, implicating the potential of the gut microbiome in stratification and refined management of obesity.

Microbiota Management for Effective Disease Suppression: A Systematic Comparison between Soil and Mammals Gut

Both soil and the human gut support vast microbial biodiversity, in which the microbiota plays critical roles in regulating harmful organisms. However, the functional link between microbiota taxonomic compositions and disease suppression has not been explained yet. Here, we provide an overview of pathogen regulation in soil and mammals gut, highlighting the differences and the similarities between the two systems. First, we provide a review of the ecological mechanisms underlying the regulation of soil and pathogens, as well as the link between disease suppression and soil health. Particular emphasis is thus given to clarifying how soil and the gut microbiota are associated with organic amendment and the human diet, respectively. Moreover, we provide several insights into the importance of organic amendment and diet composition in shaping beneficial microbiota as an efficient way to support crop productivity and human health. This review also discusses novel ways to functionally characterize organic amendments and the proper operational combining of such materials with beneficial microbes for stirring suppressive microbiota against pathogens. Furthermore, specific examples are given to describe how agricultural management practices, including the use of antibiotics and fumigants, hinder disease suppression by disrupting microbiota structure, and the potentiality of entire microbiome transplant. We conclude by discussing general strategies to promote soil microbiota biodiversity, the connection with plant yield and health, and their possible integration through a “One Health” framework.

Diffuse Recalcitrant Osteomyelitis and Joint Septicemia Because of Bowel Perforation Secondary to Gunshot Injury: A Case Report

CASE

A previously healthy 22-year-old man was brought into the emergency department after sustaining a low-velocity, civilian gunshot wound to the abdomen that perforated the bowel. Over the next 300 days, he would be admitted and discharged multiple times, requiring a total of 48 debridements, 23 different antimicrobials in 81 unique combinations, and had 18 different microbes cultured from various sites in bone, joint, and blood. Multiorganism bacteremia and fungemia culminated in above-knee amputation because of progression of infection, all in a nonimmunocompromised host.

CONCLUSION

Despite following clinical guidelines, patients can still fail evidence-based treatment algorithms. A humbling reminder is that medicine is never one-size-fits-all.

APB-13 improves the adverse outcomes caused by TGEV infection by correcting the intestinal microbial disorders in piglets

Porcine transmissible gastroenteritis virus (TGEV) is an enteric coronavirus that has caused high morbidity and mortality of piglets worldwide. Previous studies have shown that the TGEV can lead to severe diarrhoea, vomiting and dehydration in 2-week-old piglets and weaned piglets, resulting in a large number of piglet deaths. Antimicrobial peptides have broad-spectrum antimicrobial activity and a strong killing effect on bacteria, especially on the drug-resistant pathogenic bacteria, and it has attracted broad concern. However, there are very few reports on the effect of APB-13 (an antimicrobial peptide) on the intestinal microbes of piglets infected with TGEV. In this study, 16S rRNA gene sequencing was used to compare the microbial phylum and the genus of piglet's enteric microorganism in different experimental groups, and to predict the metabolic function of the microbial flora. At the same time, the apparent digestibility of nutrients, digestive enzyme activity, daily weight gain and survival rate were also measured. TGEV infection could cause the imbalance of intestinal microbes in piglets, and increase of the relative abundance of Proteobacteria, and decrease of the relative abundance of Firmicutes, Bacteroidetes and Actinobacteri. With the addition of APB-13, this problem can be alleviated, which can reduce the relative abundance of Proteobacteria and improve the balance of intestinal microorganisms. At the microbial genus level, after adding APB-13, the relative abundance of Catenibacterium, Enterobacter and Streptococcus in the intestinal tract of piglets infected with TGEV showed significant decrease, while the relative abundance of Lactobacillus and Ruminococcus increased. Finally, we found that APB-13 can significantly increase the activity of digestive enzyme in the intestinal tract of piglet, thereby improving the apparent digestibility of nutrients and the growth performance of piglets. This study demonstrates that APB-13 can alleviate the adverse outcomes caused by TGEV infection by correcting the intestinal microbial disorders.

Obesity-Related Gut Microbiota Aggravates Alveolar Bone Destruction in Experimental Periodontitis through Elevation of Uric Acid

Obesity is a risk factor for periodontal disease (PD). Initiation and progression of PD are modulated by complex interactions between oral dysbiosis and host responses. Although obesity is associated with increased susceptibility to bacterial infection, the detailed mechanisms that connect obesity and susceptibility to PD remain elusive. Using fecal microbiota transplantation and a ligature-induced PD model, we demonstrated that gut dysbiosis-associated metabolites from high-fat diet (HFD)-fed mice worsen alveolar bone destruction. Fecal metabolomics revealed elevated purine degradation pathway activity in HFD-fed mice, and recipient mice had elevated levels of serum uric acid upon PD induction. Furthermore, PD induction caused more severe bone destruction in hyperuricemic than normouricemic mice, and the worsened bone destruction was completely abrogated by allopurinol, a xanthine oxidase inhibitor. Thus, obesity increases the risk of PD by increasing production of uric acid mediated by gut dysbiosis.

Microbiome analysis reveals the alterations in gut microbiota in different intestinal segments of Yimeng black goats

Mounting evidence revealed the importance of gut microbiota in host metabolism, immunity and physiology, and health. Yimeng black goats (YBGs) mainly distributed in Shandong province of China, displayed a complicated intestinal microecosystem, but studies of its gut microbiota are still insufficient to report. Therefore, this study was performed with an objective to characterize the intestinal microbial community structure and diversity in the small intestine (duodenum, jejunum and ileum) and cecum of YBGs and investigated the variability of gut microbiota of different intestinal segments. A total of 12 intestinal samples were collected from YBGs for high-throughput sequencing analysis based on V3-V4 variable region of 16S rRNA genes. Our results revealed alterations in gut microbial composition with obvious differences in relative abundance between the different intestinal segments. Additionally, small intestine including duodenum, jejunum and ileum not only displayed higher species abundance and diversity than cecum but also showed a significant difference among the main components of gut microbiota based on the analytical results of alpha and beta diversities. At the phylum level, Firmicutes and Proteobacteria were the most preponderant phyla in all the samples regardless of intestinal sites. Moreover, the microbiota in small intestine was significantly different from cecum, which were characterized by the higher relative abundance of Butyrivibrio_2, Megasphaera, Halomonas, Delftia, Hydrogenophaga, Limnobacter, Pseudoxanthomonas, Novosphingobium, Janibacter and Erythrobacter, whereas the levels of Butyricicoccus, unidentified_Lachnospiraceae, Fusicatenibacter, Akkermansia, Ruminococcaceae_NK4A214_group and Lactobacillus were lower. Overall, this study first characterized the profile of gut microbiota composition in different intestinal sites and provide better insight into intestinal microbial community structure and diversity of YBGs.

Probiotics for preventing gestational diabetes

BACKGROUND

Gestational diabetes mellitus (GDM) is associated with a range of adverse pregnancy outcomes for mother and infant. The prevention of GDM using lifestyle interventions has proven difficult. The gut microbiome (the composite of bacteria present in the intestines) influences host inflammatory pathways, glucose and lipid metabolism and, in other settings, alteration of the gut microbiome has been shown to impact on these host responses. Probiotics are one way of altering the gut microbiome but little is known about their use in influencing the metabolic environment of pregnancy. This is an update of a review last published in 2014.

OBJECTIVES

To systematically assess the effects of probiotic supplements used either alone or in combination with pharmacological and non-pharmacological interventions on the prevention of GDM.

SEARCH METHODS

We searched Cochrane Pregnancy and Childbirth's Trials Register, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform (ICTRP) (20 March 2020), and reference lists of retrieved studies.

SELECTION CRITERIA

Randomised and cluster-randomised trials comparing the use of probiotic supplementation with either placebo or diet for the prevention of the development of GDM. Cluster-randomised trials were eligible for inclusion but none were identified. Quasi-randomised and cross-over design studies were not eligible for inclusion in this review. Studies presented only as abstracts with no subsequent full report of study results were only included if study authors confirmed that data in the abstract came from the final analysis. Otherwise, the abstract was left awaiting classification.

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed study eligibility, extracted data and assessed risk of bias of included studies. Data were checked for accuracy.

MAIN RESULTS

In this update, we included seven trials with 1647 participants. Two studies were in overweight and obese women, two in obese women and three did not exclude women based on their weight. All included studies compared probiotics with placebo. The included studies were at low risk of bias overall except for one study that had an unclear risk of bias. We excluded two studies, eight studies were ongoing and three studies are awaiting classification. Six included studies with 1440 participants evaluated the risk of GDM. It is uncertain if probiotics have any effect on the risk of GDM compared to placebo (mean risk ratio (RR) 0.80, 95% confidence interval (CI) 0.54 to 1.20; 6 studies, 1440 women; low-certainty evidence). The evidence was low certainty due to substantial heterogeneity and wide CIs that included both appreciable benefit and appreciable harm. Probiotics increase the risk of pre-eclampsia compared to placebo (RR 1.85, 95% CI 1.04 to 3.29; 4 studies, 955 women; high-certainty evidence) and may increase the risk of hypertensive disorders of pregnancy (RR 1.39, 95% CI 0.96 to 2.01, 4 studies, 955 women), although the CIs for hypertensive disorders of pregnancy also indicated probiotics may have no effect. There were few differences between groups for other primary outcomes. Probiotics make little to no difference in the risk of caesarean section (RR 1.00, 95% CI 0.86 to 1.17; 6 studies, 1520 women; high-certainty evidence), and probably make little to no difference in maternal weight gain during pregnancy (MD 0.30 kg, 95% CI -0.67 to 1.26; 4 studies, 853 women; moderate-certainty evidence). Probiotics probably make little to no difference in the incidence of large-for-gestational age infants (RR 0.99, 95% CI 0.72 to 1.36; 4 studies, 919 infants; moderate-certainty evidence) and may make little to no difference in neonatal adiposity (2 studies, 320 infants; data not pooled; low-certainty evidence). One study reported adiposity as fat mass (MD -0.04 kg, 95% CI -0.12 to 0.04), and one study reported adiposity as percentage fat (MD -0.10%, 95% CI -1.19 to 0.99). We do not know the effect of probiotics on perinatal mortality (RR 0.33, 95% CI 0.01 to 8.02; 3 studies, 709 infants; low-certainty evidence), a composite measure of neonatal morbidity (RR 0.69, 95% CI 0.36 to 1.35; 2 studies, 623 infants; low-certainty evidence), or neonatal hypoglycaemia (mean RR 1.15, 95% CI 0.69 to 1.92; 2 studies, 586 infants; low-certainty evidence). No included studies reported on perineal trauma, postnatal depression, maternal and infant development of diabetes or neurosensory disability.

AUTHORS' CONCLUSIONS

Low-certainty evidence from six trials has not clearly identified the effect of probiotics on the risk of GDM. However, high-certainty evidence suggests there is an increased risk of pre-eclampsia with probiotic administration. There were no other clear differences between probiotics and placebo among the other primary outcomes. The certainty of evidence for this review's primary outcomes ranged from low to high, with downgrading due to concerns about substantial heterogeneity between studies, wide CIs and low event rates. Given the risk of harm and little observed benefit, we urge caution in using probiotics during pregnancy. The apparent effect of probiotics on pre-eclampsia warrants particular consideration. Eight studies are currently ongoing, and we suggest that these studies take particular care in follow-up and examination of the effect on pre-eclampsia and hypertensive disorders of pregnancy. In addition, the underlying potential physiology of the relationship between probiotics and pre-eclampsia risk should be considered.

Causal effects in microbiomes using interventional calculus

Causal inference in biomedical research allows us to shift the paradigm from investigating associational relationships to causal ones. Inferring causal relationships can help in understanding the inner workings of biological processes. Association patterns can be coincidental and may lead to wrong conclusions about causality in complex systems. Microbiomes are highly complex, diverse, and dynamic environments. Microbes are key players in human health and disease. Hence knowledge of critical causal relationships among the entities in a microbiome, and the impact of internal and external factors on microbial abundance and their interactions are essential for understanding disease mechanisms and making appropriate treatment recommendations. In this paper, we employ causal inference techniques to understand causal relationships between various entities in a microbiome, and to use the resulting causal network to make useful computations. We introduce a novel pipeline for microbiome analysis, which includes adding an outcome or "disease" variable, and then computing the causal network, referred to as a "disease network", with the goal of identifying disease-relevant causal factors from the microbiome. Internventional techniques are then applied to the resulting network, allowing us to compute a measure called the causal effect of one or more microbial taxa on the outcome variable or the condition of interest. Finally, we propose a measure called causal influence that quantifies the total influence exerted by a microbial taxon on the rest of the microiome. Our pipeline is robust, sensitive, different from traditional approaches, and able to predict interventional effects without any controlled experiments. The pipeline can be used to identify potential eubiotic and dysbiotic microbial taxa in a microbiome. We validate our results using synthetic data sets and using results on real data sets that were previously published.

Polychlorinated biphenyls altered gut microbiome in CAR and PXR knockout mice exhibiting toxicant-associated steatohepatitis

Polychlorinated biphenyls (PCBs) are persistent organic pollutants associated with non-alcoholic fatty liver disease (NAFLD). Previously, we demonstrated that the PCB mixture, Aroclor1260, exacerbated NAFLD, reflective of toxicant-associated steatohepatitis, in diet-induced obese mice, in part through pregnane-xenobiotic receptor (PXR) and constitutive androstane receptor (CAR) activation. Recent studies have also reported PCB-induced changes in the gut microbiome that consequently impact NAFLD. Therefore, the objective of this study is to examine PCB effects on the gut-liver axis and characterize the role of CAR and PXR in microbiome alterations. C57Bl/6 (wildtype, WT), CAR and PXR knockout mice were fed a high fat diet and exposed to Aroclor1260 (20 mg/kg, oral gavage, 12 weeks). Metagenomics analysis of cecal samples revealed that CAR and/or PXR ablation increased bacterial alpha diversity regardless of exposure status. CAR and PXR ablation also increased bacterial composition (beta diversity) versus WT; Aroclor1260 altered beta diversity only in WT and CAR knockouts. Distinct changes in bacterial abundance at different taxonomic levels were observed between WT and knockout groups; however Aroclor1260 had modest effects on bacterial abundance within each genotype. Notably, both knockout groups displayed increased Actinobacteria and Verrucomicrobia abundance. In spite of improved bacterial diversity, the knockout groups however failed to show protection from PCB-induced hepato- and intestinal- toxicity including decreased mRNA levels of ileal permeability markers (occludin, claudin3). In summary, CAR and PXR ablation significantly altered gut microbiome in diet-induced obesity while Aroclor1260 compromised intestinal integrity in knockout mice, implicating interactions between PCBs and CAR, PXR on the gut-liver axis.

Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

Efficacy of metformin and fermentable fiber combination therapy in adolescents with severe obesity and insulin resistance: study protocol for a double-blind randomized controlled trial

Background

Accumulating evidence suggests that the metabolic effects of metformin and fermentable fibers are mediated, in part, through diverging or overlapping effects on the composition and metabolic functions of the gut microbiome. Pre-clinical animal models have established that the addition of fiber to metformin monotherapy improves glucose tolerance. However, possible synergistic effects of combination therapy (metformin plus fiber) have not been investigated in humans. Moreover, the underlying mechanisms of synergy have yet to be elucidated. The aim of this study is to compare in adolescents with obesity the metabolic effects of metformin and fermentable fibers in combination with those of metformin or fiber alone. We will also determine if therapeutic responses correlate with compositional and functional features of the gut microbiome.

Methods

This is a parallel three-armed, double-blinded, randomized controlled trial. Adolescents (aged 12–18 years) with obesity, insulin resistance (IR), and a family history of type 2 diabetes mellitus (T2DM) will receive either metformin (850 mg p.o. twice/day), fermentable fibers (35 g/day), or a combination of metformin plus fiber for 12 months. Participants will be seen at baseline, 3, 6, and 12 months, with a phone follow-up at 1 and 9 months. Primary and secondary outcomes will be assessed at baseline, 6, and 12 months. The primary outcome is change in IR estimated by homeostatic model assessment of IR; key secondary outcomes include changes in the Matsuda index, oral disposition index, body mass index z-score, and fat mass to fat-free mass ratio. To gain mechanistic insight, endpoints that reflect host-microbiota interactions will also be assessed: obesity-related immune, metabolic, and satiety markers; humoral metabolites; and fecal microbiota composition, short-chain fatty acids, and bile acids.

Discussion

This study will compare the potential metabolic benefits of fiber with those of metformin in adolescents with obesity, determine if metformin and fiber act synergistically to improve IR, and elucidate whether the metabolic benefits of metformin and fiber associate with changes in fecal microbiota composition and the output of health-related metabolites. This study will provide insight into the potential role of the gut microbiome as a target for enhancing the therapeutic efficacy of emerging treatments for T2DM prevention.

Trial registration

ClinicalTrials.gov NCT04578652. Registered on 8 October 2020.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13063-021-05060-8.

Genetic Background Shapes Phenotypic Response to Diet for Adiposity in the Collaborative Cross

Defined as chronic excessive accumulation of adiposity, obesity results from long-term imbalance between energy intake and expenditure. The mechanisms behind how caloric imbalance occurs are complex and influenced by numerous biological and environmental factors, especially genetics, and diet. Population-based diet recommendations have had limited success partly due to the wide variation in physiological responses across individuals when they consume the same diet. Thus, it is necessary to broaden our understanding of how individual genetics and diet interact relative to the development of obesity for improving weight loss treatment. To determine how consumption of diets with different macronutrient composition alter adiposity and other obesity-related traits in a genetically diverse population, we analyzed body composition, metabolic rate, clinical blood chemistries, and circulating metabolites in 22 strains of mice from the Collaborative Cross (CC), a highly diverse recombinant inbred mouse population, before and after 8 weeks of feeding either a high protein or high fat high sucrose diet. At both baseline and post-diet, adiposity and other obesity-related traits exhibited a broad range of phenotypic variation based on CC strain; diet-induced changes in adiposity and other traits also depended largely on CC strain. In addition to estimating heritability at baseline, we also quantified the effect size of diet for each trait, which varied by trait and experimental diet. Our findings identified CC strains prone to developing obesity, demonstrate the genotypic and phenotypic diversity of the CC for studying complex traits, and highlight the importance of accounting for genetic differences when making dietary recommendations.

Is Technical-Grade Chlordane an Obesogen?

The prevalence of obesity has tripled in recent decades and is now considered an alarming public health problem. In recent years, a group of endocrine disruptors, known as obesogens, have been directly linked to the obesity epidemic. Its etiology is generally associated with a sedentary lifestyle, a high-fat diet and genetic predisposition, but environmental factors, such as obesogens, have also been reported as contributors for this pathology. In brief, obesogens are exogenous chemical compounds that alter metabolic processes and/or energy balance and appetite, thus predisposing to weight gain. Although this theory is still recent, the number of compounds with suspected obesogenic activity has steadily increased over the years, though many of them remain a matter of debate. Technical-grade chlordane is an organochlorine pesticide widely present in the environment, albeit at low concentrations. Highly lipophilic compounds can be metabolized by humans and animals into more toxic and stable compounds that are stored in fat tissue and consequently pose a danger to the human body, including the physiology of adipose tissue, which plays an important role in weight regulation. In addition, technical-grade chlordane is classified as a persistent organic pollutant, a group of chemicals whose epidemiological studies are associated with metabolic disorders, including obesity. Herein, we discuss the emerging roles of obesogens as threats to public health. We particularly discuss the relevance of chlordane persistence in the environment and how its effects on human and animal health provide evidence for its role as an endocrine disruptor with possible obesogenic activity.

Gut Microbiota Profile and Changes in Body Weight in Elderly Subjects with Overweight/Obesity and Metabolic Syndrome

Gut microbiota is essential for the development of obesity and related comorbidities. However, studies describing the association between specific bacteria and obesity or weight loss reported discordant results. The present observational study, conducted within the frame of the PREDIMED-Plus clinical trial, aims to assess the association between fecal microbiota, body composition and weight loss, in response to a 12-month lifestyle intervention in a subsample of 372 individuals (age 55–75) with overweight/obesity and metabolic syndrome. Participants were stratified by tertiles of baseline body mass index (BMI) and changes in body weight after 12-month intervention. General assessments, anthropometry and biochemical measurements, and stool samples were collected. 16S amplicon sequencing was performed on bacterial DNA extracted from stool samples and microbiota analyzed. Differential abundance analysis showed an enrichment of Prevotella 9, Lachnospiraceae UCG-001 and Bacteroides, associated with a higher weight loss after 12-month of follow-up, whereas in the cross-sectional analysis, Prevotella 2 and Bacteroides were enriched in the lowest tertile of baseline BMI. Our findings suggest that fecal microbiota plays an important role in the control of body weight, supporting specific genera as potential target in personalized nutrition for obesity management. A more in-depth taxonomic identification method and the need of metabolic information encourages to further investigation.

Effects of gut microbiota on atherosclerosis through hydrogen sulfide

Cardiovascular diseases are the leading cause of death and morbidity worldwide. Atherosclerotic cardiovascular disease (ASCVD) is affected by both environmental and genetic factors. Microenvironmental disorders of the human gut flora are associated with a variety of health problems, not only gastrointestinal diseases, such as inflammatory bowel disease, but also extralintestinal organs. Hydrogen sulfide (H₂S) is the third gas signaling molecule other than nitric oxide and carbon monoxide. In the cardiovascular system, H₂S plays important roles in the regulation of blood pressure, angiogenesis, smooth muscle cell proliferation and apoptosis, anti-oxidative stress, cardiac functions. This review is aiming to explore the potential role of gut microbiota in the development of atherosclerosis through hydrogen sulfide production as a novel therapeutic direction for atherosclerosis.

Coarse Cereals and Legume Grains Exert Beneficial Effects through Their Interaction with Gut Microbiota: A Review

Coarse cereals and legume grains (CCLGs) are rich in specific macro- and functional elements that are considered important dietary components for maintaining human health. Therefore, determining the precise nutritional mechanism involved in exerting the health benefits of CCLGs can help understand dietary nutrition in a better manner. Evidence suggests that gut microbiota play a crucial role in the function of CCLGs via their complicated interplay with CCLGs. First, CCLGs modulate gut microbiota and function. Second, gut microbiota convert CCLGs into compounds that perform different functions. Third, gut microbiota mediate interactions among different CCLG components. Therefore, using gut microbiota to expound the nutritional mechanism of CCLGs is important for future studies. A precise and rapid gut microbiota research model is required to screen and evaluate the quality of CCLGs. The outcomes of such research may promote the rapid discovery, classification, and evaluation of CCLG resources, thereby opening a new opportunity to guide nutrition-based development of CCLG products.

Comparative Analysis of the Gut Microbial Communities of the Eurasian Kestrel (Falco tinnunculus) at Different Developmental Stages

The gut microflora play a very important role in the life of animals. Although an increasing number of studies have investigated the gut microbiota of birds in recent years, there is a lack of research work on the gut microbiota of wild birds, especially carnivorous raptors, which are thought to be pathogen vectors. There are also a lack of studies focused on the dynamics of the gut microbiota during development in raptors. In this study, 16S rRNA gene amplicon high-throughput sequencing was used to analyze the gut microbiota community composition of a medium-sized raptor, the Eurasian Kestrel (Falco tinnunculus), and to reveal stage-specific signatures in the gut microbiota of nestlings during the pre-fledging period. Moreover, differences in the gut microbiota between adults and nestlings in the same habitat were explored. The results indicated that the Eurasian Kestrel hosts a diverse assemblage of gut microbiota. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the primary phyla shared within the guts of adults and chicks. However, adults harbored higher abundances of Proteobacteria while nestlings exhibited higher abundances of Firmicutes and Actinobacteria, and consequently the majority of dominant genera observed in chicks differed from those in adults. Although no significant differences in diversity were observed across the age groups during nestling ontogeny, chicks from all growth stages harbored richer and more diverse bacterial communities than adults. In contrast, the differences in gut microbial communities between adults and younger nestlings were more pronounced. The gut microbes of the nestlings in the last growth stage were converged with those of the adults. This study provides basic reference data for investigations of the gut microbiota community structure of wild birds and deepens our understanding of the dynamics of the gut microflora during raptor development.

Duodenal Metatranscriptomics to Define Human and Microbial Functional Alterations Associated with Severe Obesity: A Pilot Study

Obesity is a multifactorial disorder, and the gut microbiome has been suggested to contribute to its onset. In order to better clarify the role of the microbiome in obesity, we evaluated the metatranscriptome in duodenal biopsies from a cohort of 23 adult severely obese and lean control subjects using next generation sequencing. Our aim was to provide a general picture of the duodenal metatranscriptome associated with severe obesity. We found altered expressions of human and microbial genes in the obese compared to lean subjects, with most of the gene alterations being present in the carbohydrate, protein, and lipid metabolic pathways. Defects were also present in several human genes involved in epithelial intestinal cells differentiation and function, as well as in the immunity/inflammation pathways. Moreover, the microbial taxa abundance inferred by our transcriptomic data differed in part from the data that we previously evaluated by 16S rRNA in 13/23 individuals of our cohort, particularly concerning the Firmicutes and Proteobacteria phyla abundances. In conclusion, our pilot study provides the first taxonomic and functional characterization of duodenal microbiota in severely obese subjects and lean controls. Our findings suggest that duodenal microbiome and human genes both play a role in deregulating metabolic pathways, likely affecting energy metabolism and thus contributing to the obese phenotype.

Cross talk between drug-resistant epilepsy and the gut microbiome

One-third of epilepsy patients have drug-resistant epilepsy (DRE), which is often complicated by polydrug toxicity and psychiatric and cognitive comorbidities. Advances in understanding the microbiome and gut-brain-axis are likely to shed light on epilepsy pathogenesis, anti-seizure medication (ASM) resistance, and potential therapeutic targets. Gut dysbiosis is associated with inflammation, blood-brain barrier disruption, and altered neuromodulators. High-throughput and metagenomic sequencing has advanced the characterization of microbial species and functional pathways. DRE patients show altered gut microbiome composition compared to drug-sensitive patients and healthy controls. The ketogenic and modified Atkins diets can reduce seizures in some patients with DRE. These low-carbohydrate dietary therapies alter the taxonomic and functional composition of the gut microbiome, and composition varies between diet responders and nonresponders. Murine models suggest that specific phyla are necessary to confer efficacy from the diet, and antibiotic treatment may eliminate efficacy. The impact of diet might involve alterations in microbiota, promotion of select microbial interactions, and variance in brain neurotransmitter levels that then influence seizures. Understanding the mechanics of how diet manipulates seizures may suggest novel therapies. Most ASMs act on neuronal transmission via effects on ion channels and neurotransmitters. However, ASMs may also assert their effects via the gut microbiota. In animal models, the microbiota composition (eg, abundance of certain phyla) can vary with ASM active drug metabolites. Given the developing understanding of the gut microbiome in DRE, probiotics are another potential therapy. Probiotics alter the microbiota composition, and small studies suggest that these supplements can reduce seizures in some patients. DRE has enormous consequences to patients and society, and the gut microbiome holds promise as a potential therapeutic target. However, the exact mechanism and recognition of which patients are likely to be responders remain elusive. Further studies are warranted.

Bile Acids as a New Type of Steroid Hormones Regulating Nonspecific Energy Expenditure of the Body (Review)

The review is devoted to the systematization, classification, and generalization of the results of modern scientific research on the role of bile acids as a new class of steroid hormones. The paper presents the evidence for bile acid participation in the regulation of the body energy metabolism, body weight control, as well as the pathogenesis of obesity, diabetes mellitus, insulin resistance, and cardiovascular diseases. Particular attention is paid to the role of bile acids in the control of nonspecific energy expenditure of the body. The applied aspects of using the novel data about the membrane and intracellular receptors responsible for the development of hormonal regulatory effects of bile acids are analyzed. According to the authors, the modern data on the role of bile acids in the regulation of body functions allow a deeper understanding of the pathogenesis of body weight disorders and associated cardiovascular diseases. The review demonstrates promising directions in the search for specific methods of prevention and correction of these pathological conditions.

What was First, Obesity or Inflammatory Bowel Disease? What Does the Gut Microbiota Have to Do with It?

A sedentary lifestyle and inadequate nutrition often leads to disturbances in intestinal homeostasis, which may predispose people to excess body weight and metabolic syndrome. Obesity is frequently observed in patients with inflammatory bowel diseases (IBD), similar to the general population. Obesity may exert a negative effect on the course of IBD as well as reduce the response to treatment. Moreover, it may also be an additional risk factor for vein thromboembolism during the flare. In both obesity and IBD, it is of great importance to implement proper dietary ingredients that exert desirable effect on gut microbiota. The key to reducing body mass index (BMI) and alleviating the course of IBD is preserving healthy intestinal microflora.

Composition of "gold juice" using an ancient method based on intestinal microecology

Objective

To identify potentially effective bacterial components of gold juice, a traditional Chinese medicine treatment used for fecal microbiota transplantation.

Methods

Fecal samples were collected from five healthy children (two boys and three girls; mean age, 7.52 ± 2.31 years). The children had no history of antibiotic use or intestinal microecological preparation in the preceding 3 months. Fresh fecal samples were collected from children to prepare gold juice in mid-to-late November, in accordance with traditional Chinese medicine methods, then used within 7 days. Finally, 16S rDNA sequence analysis was used to identify potentially effective bacterial components of gold juice. QIIME software was used for comparisons of microbial species among gold juice, diluent, filtrate, and loess samples.

Results

Microflora of gold juice exhibited considerable changes following “ancient method” processing. Microbial components significantly differed between gold juice and filtrate samples. The gold juice analyzed in our study consisted of microbes that synthesize carbohydrates and amino acids by degrading substances, whereas the filtrate contained probiotic flora, Bacteroides, and Prevotella 9.

Conclusions

This study of microbial components in gold juice and filtrate provided evidence regarding effective bacterial components in gold juice, which may aid in clinical decisions concerning fecal microbiota transplantation.

Gut Microbiota and Intestinal Trans-Epithelial Permeability

Constant remodeling of tight junctions to regulate trans-epithelial permeability is essential in maintaining intestinal barrier functions and thus preventing diffusion of small molecules and bacteria to host systemic circulation. Gut microbiota dysbiosis and dysfunctional gut barrier have been correlated to a large number of diseases such as obesity, type 2 diabetes and inflammatory bowel disease. This led to the hypothesis that gut bacteria-epithelial cell interactions are key regulators of epithelial permeability through the modulation of tight junctions. Nevertheless, the molecular basis of host-pathogen interactions remains unclear mostly due to the inability of most in vitro models to recreate the differentiated tissue structure and components observed in the normal intestinal epithelium. Recent advances have led to the development of a novel cellular model derived from intestinal epithelial stem cells, the so-called organoids, encompassing all epithelial cell types and reproducing physiological properties of the intestinal tissue. We summarize herein knowledge on molecular aspects of intestinal barrier functions and the involvement of gut bacteria-epithelial cell interactions. This review also focuses on epithelial organoids as a promising model for epithelial barrier functions to study molecular aspects of gut microbiota-host interaction.

Omics Biomarkers in Obesity: Novel Etiological Insights and Targets for Precision Prevention

PURPOSE OF REVIEW

Omics-based technologies were suggested to provide an advanced understanding of obesity etiology and its metabolic consequences. This review highlights the recent developments in "omics"-based research aimed to identify obesity-related biomarkers.

RECENT FINDINGS

Recent advances in obesity and metabolism research increasingly rely on new technologies to identify mechanisms in the development of obesity using various "omics" platforms. Genetic and epigenetic biomarkers that translate into changes in transcriptome, proteome, and metabolome could serve as targets for obesity prevention. Despite a number of promising candidate biomarkers, there is an increased demand for larger prospective cohort studies to validate findings and determine biomarker reproducibility before they can find applications in primary care and public health. "Omics" biomarkers have advanced our knowledge on the etiology of obesity and its links with chronic diseases. They bring substantial promise in identifying effective public health strategies that pave the way towards patient stratification and precision prevention.

Natural environments in the urban context and gut microbiota in infants

The biodiversity hypothesis that contact with natural environments (e.g. native vegetation) and biodiversity, through the influence of environmental microbes, may be beneficial for human commensal microbiota has been insufficiently tested. We aimed to study the association between living near natural environments in the urban context, and gut microbiota diversity and composition in young infants. Based on data linkage between the unique Urban Primary Land and Vegetation Inventory (uPLVI) for the city of Edmonton and 355 infants in the CHILD Cohort Study, infant exposure to natural environments (any and specific types, yes/no) was determined within 500 m and 1000 m of their home residence. Gut microbiota composition and diversity at age 4 months was assessed in infant fecal samples. Adjusted for covariates, we observed a reduced odds of high microbial alpha-diversity in the gut of infants exposed to any natural environment within 500 m [Shannon index aOR (95%CI) = 0.63 (0.40, 0.98) and Simpson index = 0.63 (0.41, 0.98)]. In stratified analyses, these associations remained only among infants not breastfed or living with household pets. When doubly stratifying by these variables, the reduced likelihood of high alpha-diversity was present only among infants who were not breastfed and lived with household pets [9% of the study population, Shannon index = 0.07 (0.01, 0.49) and Simpson index = 0.11 (0.02, 0.66)]. Differences in beta-diversity was also seen (p = 0.04) with proximity to a nature space in not breastfed and pets-exposed infants. No associations were observed among infants who were fully formula-fed but without pets at home. When families and their pets had close access to a natural environment, Verrucomicrobiales colonization was reduced in the gut microbiota of formula-fed infants, the abundance of Clostridiales was depleted, whereas the abundance of Enterobacteriales was enriched. Our double-stratified results indicate that proximity to a natural environment plus pet ownership has the capacity to alter the gut microbiota of formula-fed infants. Further research is needed to replicate and better interpret these results, as well as to understand their health consequences.

Rebalancing glucolipid metabolism and gut microbiome dysbiosis by nitrate-dependent alleviation of high-fat diet-induced obesity

INTRODUCTION

High-fat diet (HFD)-induced obesity is accompanied by compromised nitric oxide (NO) signaling and gut microbiome dysregulation. Inorganic dietary nitrate, which acts as a NO donor, exerts beneficial effects on metabolic disorders. Here, we evaluated the effects of dietary nitrate on HFD-induced obesity and provided insights into the underlying mechanism.

RESEARCH DESIGN AND METHODS

To investigate the preventive effect of dietary nitrate on HFD-induced obesity, C57BL/6 mice were randomly assigned into four groups (n=10/group), including normal control diet group (normal water and chow diet), HFD group (normal water and HFD), HFD+NaNO₃ group (water containing 2 mM NaNO₃ and HFD), and HFD+NaCl group (water containing 2 mM NaCl and HFD). During the experiment, body weight was monitored and glucolipid metabolism was evaluated. The mechanism underlying the effects of nitrate on HFD-induced obesity was investigated by the following: the NO₃^--NO₂^--NO pathway; endothelial NO synthase (eNOS) and cyclic guanosine monophosphate (cGMP) levels; gut microbiota via 16SRNA analysis.

RESULTS

Dietary nitrate reduced the body weight gain and lipid accumulation in adipose and liver tissues in HFD-fed mice. Hyperlipidemia and insulin resistance caused by HFD were improved in mice supplemented with nitrate. The level of eNOS was upregulated by nitrate in the serum, liver, and inguinal adipose tissue. Nitrate, nitrite, and cGMP levels were decreased in mice fed on HFD but reversed in the HFD+NaNO₃ group. Nitrate also rebalanced the colon microbiota and promoted a normal gut microbiome profile by partially attenuating the impacts of HFD. Bacteroidales S24-7, Alistipes, Lactobacillus, and Ruminococcaceae abundances were altered, and Bacteroidales S24-7 and Alistipes abundances were higher in the HFD+NaNO₃ group than that in the HFD group.

CONCLUSIONS

Inorganic dietary nitrate alleviated HFD-induced obesity and ameliorated disrupted glucolipid metabolism via NO₃^--NO₂^--NO pathway activation and gut microbiome modulation.

The influence of the gut microbiome on obesity

Obesity is a disease with multiple environmental and genetic factors, which when combined contribute to the maintenance of an elevated body weight, thereby reducing long-term success of weight loss. The human gut microbiome is becoming a new potential contributor to obesity. Specifically, gut bacteria and their metabolites are known to affect dysbiosis, metabolism, endotoxemia, and inflammation. Many environmental and lifestyle factors can alter the gut microbiota affecting obesity. Potential therapies to alter the gut microbiota include supplementation with probiotic organisms and the use of fecal microbiota transplantation. This review will examine the growing evidence supporting the mechanisms with which the human gut microbiota may influence obesity, various influences on the microbiota, and potential therapies.

Identification of Cartilage Microbial DNA Signatures and Associations With Knee and Hip Osteoarthritis

OBJECTIVE

Alterations of the gut microbiota have been implicated in many forms of arthritis, but an examination of cartilage microbial patterns has not been performed. This study was undertaken to characterize the microbial DNA profile of articular cartilage and determine changes associated with osteoarthritis (OA).

METHODS

We performed 16S ribosomal RNA gene deep sequencing on eroded and intact cartilage samples from knee OA patients (n = 21 eroded and 21 intact samples) and hip OA patients (n = 34 eroded and 33 intact samples) and cadaver controls (n = 10 knee samples and 10 hip samples). Microbial DNA diversity was assessed, groups were compared, and metagenomic profiles were reconstructed. Confirmation was performed in an independent cohort by clade-specific quantitative polymerase chain reaction. Findings in human cartilage were compared to those in cartilage from OA-susceptible C57BL/6 (B6) mice and OA-resistant MRL/MpJ (MRL) mice. Germ-free B6 mouse cartilage was analyzed as a methodologic control.

RESULTS

Alpha diversity was reduced in human OA versus control samples (P < 0.0001), and in hip versus knee samples (P < 0.0001). Numerous clades were different in human OA versus control samples, and similar findings were noted in comparisons of murine B6 versus MRL mice. Hip samples were microbiologically distinct from knee samples. OA microbial DNA demonstrated increased gram-negative constituents (P = 0.02). Functional analysis demonstrated increases in lipopolysaccharide production (P = 9.9 × 10-3 ), phosphatidylinositol signaling (P = 4.2 × 10-4 ), and nitrogen metabolism (P = 8 × 10-3 ) and decreases in sphingolipid metabolism (P = 7.7 × 10-4 ) associated with OA.

CONCLUSION

Our study reveals a microbial DNA signature in human and mouse cartilage. Alterations in this signature, including increases in gram-negative constituents, occur during the development and progression of human OA. Furthermore, our findings indicate that strain-specific signatures exist within mouse cartilage that mirror human patterns. Further study of the establishment and potential pathogenic role of these DNA signatures is needed.

The Influence of the Gut Microbiome on Obesity in Adults and the Role of Probiotics, Prebiotics, and Synbiotics for Weight Loss

The link between the gut microbiome and obesity is not well defined. Understanding of the role of the gut microbiome in weight and health management may lead to future revolutionary changes for treating obesity. This review examined the relationship between obesity and the gut microbiome, and the role of probiotics, prebiotics, and synbiotics for preventing and treating obesity. We used PubMed and Google Scholar to collect appropriate articles for the review. We showed that the gut microbiome has an impact on nutrient metabolism and energy expenditure. Moreover, different modalities of obesity treatment have been shown to change the diversity and composition of the gut microbiome; this raises questions about the role these changes may play in weight loss. In addition, studies have shown that supplementation with probiotics, prebiotics, and synbiotics may alter the secretion of hormones, neurotransmitters, and inflammatory factors, thus preventing food intake triggers that lead to weight gain. Further clinical studies are needed to better understand how different species of bacteria in the gut microbiome may affect weight gain, and to determine the most appropriate doses, compositions, and regimens of probiotics, prebiotics, and synbiotics supplementation for long-term weight control.

Comparison of the Gut Microbiota Between Pulsatilla Decoction and Levofloxacin Hydrochloride Therapy on Escherichia coli Infection

Gut microbiota serves as a critical indicator for gut health during treatment of pathogenic bacterial infection. Both Pulsatilla Decoction (abbreviated to PD, a traditional Chinese medicine compound) and Levofloxacin Hydrochloride (LVX) were known to have therapeutic effects to intestinal infectious disease. However, the changes of gut microbiota after PD or LVX treatment remain unclear. Herein, this work aimed to investigate the changes of intestinal flora after PD or LVX therapy of Escherichia coli infection in rats. Results revealed that PD exhibited a valid therapeutic approach for E. coli infection via the intestinal protection, as well as the inhibited release of IL-8 and ICAM-1. Besides, PD was beneficial to rebuild the gut microbiota via restoring Bacteroidetes spp in the composition of the gut microbiota. Comparatively, LVX treatment promoted the infection and ravaged gut microbiota by significantly decreasing Bacteroidetes and increasing Firmicutes. These findings not only highlight the mechanism of Chinese herbal formula, but extend the application of PD as veterinary medicine, feed additive and pre-mixing agent for improving the production of animal derived foods.

The effects of 6 mo of supplementation with probiotics and synbiotics on gut microbiota in the adults with prediabetes: A double blind randomized clinical trial

OBJECTIVES

The evidence of 16S rRNA genes in the gut microbiota distinguished a higher Firmicutes-to-Bacteroidetes ratio in individuals who were obese and had diabetes than in a healthy cohort. So, it seems that the modulation of intestinal microbial ecology by pro-/pre-/synbiotics may contribute to the progression and prevention of metabolic diseases. The aim of this study was to assess the effects of probiotics and synbiotic supplementation on the modification of the intestinal microbiome in adults with prediabetes.

METHODS

In a randomized, double-blinded, placebo-controlled clinical trial, 120 patients with prediabetes were randomly assigned to consume 6 g/d of either a placebo containing maltodextrin (control) or multispecies probiotic or inulin-based synbiotic for 6 mo. Fecal samples were obtained at baseline and after 6 mo of supplementation. Dietary intake was assessed throughout the study (at baseline and after 3 and 6 mo). Total energy, macronutrients, and dietary fiber were calculated using a dietary program Nutritionist 4. DNA was extracted from fecal samples and the numbers of Clostridium perfringens (the represent of phylum Firmicutes), Bacteroides fragilis (the representative of Bacteroidetes) and Escherichia coli (as universal bacteria) were determined by quantitative real-time polymerase chain reactions (qPCR). The changes in the relative abundance of the two fecal bacteria before and after supplementation were analyzed and compared within and between groups.

RESULTS

There were no significant changes in dietary intake during the study. Six mo of supplementation with probiotics resulted in a statistically significant increase in the abundance of the B. fragilis-to-E.coli ratio (mean difference [MD] ± SE 0.47 ± 0.37, P = 0.04) and decrease of the relative proportion of Firmicutes-to-Bacteroidetes representatives (MD ± SE -118.8 ± 114.6, P = 0.02). Synbiotic had no significant effect on the changes in the bacteria. There were no significant differences between the three groups.

CONCLUSION

The results of this study suggest that manipulation of the human gut microbiome by using probiotics could provide a potential therapeutic approach in the prevention and management of obesity and metabolic disorders such as diabetes.

Microbial Adaptation Due to Gastric Bypass Surgery: The Nutritional Impact

Bariatric surgery leads to sustained weight loss and the resolution of obesity-related comorbidities. Recent studies have suggested that changes in gut microbiota are associated with the weight loss induced by bariatric surgery. Several studies have observed major changes in the microbial composition following gastric bypass surgery. However, there are inconsistencies between the reported alterations in microbial compositions in different studies. Furthermore, it is well established that diet is an important factor shaping the composition and function of intestinal microbiota. However, most studies on gastric bypass have not assessed the impact of dietary intake on the microbiome composition in general, let alone the impact of restrictive diets prior to bariatric surgery, which are recommended for reducing liver fat content and size. Thus, the relative impact of bariatric surgery on weight loss and gut microbiota remains unclear. Therefore, this review aims to provide a deeper understanding of the current knowledge of the changes in intestinal microbiota induced by bariatric surgery considering pre-surgical nutritional changes.

Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing

The gut microbiota may have an impact on obesity. To date, the majority of studies in obese patients reported microbiota composition in stool samples. The aim of this study was to investigate the duodenal mucosa dysbiosis in adult obese individuals from Campania, a region in Italy with a very high percentage of obese people, to highlight microbial taxa likely associated with obesity. Duodenum biopsies were taken during upper gastrointestinal endoscopy in 19 obese (OB) and 16 lean control subjects (CO) and microbiome studied by 16S rRNA gene sequencing. Duodenal microbiome in our groups consisted of six phyla: Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Proteobacteria (51.1% vs. 40.1%) and Firmicutes (33.6% vs. 44.9%) were significantly (p < 0.05) more and less abundant in OB compared with CO, respectively. Oribacterium asaccharolyticum, Atopobium parvulum and Fusobacterium nucleatum were reduced (p < 0.01) and Pseudomonadales were increased (p < 0.05) in OB compared with CO. Receiver operating characteristic curve analysis showed Atopobium and Oribacterium genera able to discriminate with accuracy (power = 75% and 78%, respectively) OB from CO. In conclusion, increased Proteobacteria and decreased Firmicutes (Lachnospiraceae) characterized the duodenal microbiome of obese subjects. These data direct to further studies to evaluate the functional role of the dysbiotic-obese-associated signature.

An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome

Our understanding of the human gut microbiome has grown exponentially. Advances in genome sequencing technologies and metagenomics analysis have enabled researchers to study microbial communities and their potential function within the context of a range of human gut related diseases and disorders. However, up until recently, much of this research has focused on characterizing the gut microbiological community structure and understanding its potential through system wide (meta) genomic and transcriptomic-based studies. Thus far, the functional output of these microbiomes, in terms of protein and metabolite expression, and within the broader context of host-gut microbiome interactions, has been limited. Furthermore, these studies highlight our need to address the issues of individual variation, and of samples as proxies. Here we provide a perspective review of the recent literature that focuses on the challenges of exploring the human gut microbiome, with a strong focus on an integrated perspective applied to these themes. In doing so, we contextualize the experimental and technical challenges of undertaking such studies and provide a framework for capitalizing on the breadth of insight such approaches afford. An integrated perspective of the human gut microbiome and the linkages to human health will pave the way forward for delivering against the objectives of precision medicine, which is targeted to specific individuals and addresses the issues and mechanisms in situ.

Neuropeptides in gut-brain axis and their influence on host immunity and stress

In recent decades, neuropeptides have been found to play a major role in communication along the gut-brain axis. Various neuropeptides are expressed in the central and peripheral nervous systems, where they facilitate the crosstalk between the nervous systems and other major body systems. In addition to being critical to communication from the brain in the nervous systems, neuropeptides actively regulate immune functions in the gut in both direct and indirect ways, allowing for communication between the immune and nervous systems. In this mini review, we discuss the role of several neuropeptides, including calcitonin gene-related peptide (CGRP), pituitary adenylate cyclase-activating polypeptide (PACAP), corticotropin-releasing hormone (CRH) and phoenixin (PNX), in the gut-brain axis and summarize their functions in immunity and stress. We choose these neuropeptides to highlight the diversity of peptide communication in the gut-brain axis.

Beneficial Effects of Lactobacillus plantarum Strains on Non-Alcoholic Fatty Liver Disease in High Fat/High Fructose Diet-Fed Rats

Emerging evidence suggests that probiotics are beneficial in non-alcoholic fatty liver disease (NAFLD). This study aimed to explore the effects of two Lactobacillus plantarum strains, ATG-K2 and ATG-K6 (isolated from Korean fermented cabbage), in a rat model of high fat/high fructose (HF/HF) diet-induced NAFLD. Rats with NAFLD were randomized into four groups (HF/HF diet control, (HC); HF/HF diet with silymarin, (PC); HF/HF diet with ATG-K2, (K2); and HF/HF diet with ATG-K6, (K6)) with healthy rats on a normal diet serving as the negative control. After treatment, histopathological and biochemical analyses of the blood and liver tissue were conducted. In addition, fecal microbiota was analyzed using the MiSeq platform. Compared with HC rats, K2 and K6 rats experienced significantly lower body weight gain, displayed decreased hepatic lipid accumulation, had lower serum levels of aspartate aminotransferase and alanine aminotransferase, and showed increased antioxidant enzyme activities. Moreover, de novo lipogenesis-related genes were downregulated following K2 and K6 administration. The fecal microbiota of K2 and K6 rats contained a higher proportion of Bacteriodetes and a lower proportion of Fimicutes than that of HC rats. Taken together, our results suggest that L. plantarum strains ATG-K2 and ATG-K6 are potential therapeutic agents for NAFLD.

Metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity in mice fed with conjugated linoleic acid (CLA)

In this study, a high fat diet induced obesity mouse model (DIO) was used to investigate the modulatory effect of high purity conjugated linoleic acid (CLA) on the intestinal microbiota.