A meta-metabolome network of carbohydrate metabolism: interactions between gut microbiota and host. Biochem Biophys Res Commun. 2012;428:278-284. [PMID: 23085046 DOI: 10.1016/j.bbrc.2012.10.045]

Effects of environmentally relevant concentrations of florfenicol on the glucose metabolism system, intestinal microbiome, and liver metabolome of zebrafish

Florfenicol, a widely used veterinary antibiotic, has now been frequently detected in various water environments and human urines, with high concentrations. Accordingly, the ecological risks and health hazards of florfenicol are attracting increasing attention. In recent years, antibiotic exposure has been implicated in the disruption of animal glucose metabolism. However, the specific effects of florfenicol on the glucose metabolism system and the underlying mechanisms are largely unknown. Herein, zebrafish as an animal model were exposed to environmentally relevant concentrations of florfenicol for 28 days. Using biochemical and molecular analyses, we found that exposure to florfenicol disturbed glucose homeostasis, as evidenced by the abnormal levels of blood glucose and hepatic/muscular glycogen, and the altered expression of genes involved in glycogenolysis, gluconeogenesis, glycogenesis, and glycolysis. Considering the efficient antibacterial activity of florfenicol and the crucial role of intestinal flora in host glucose metabolism, we then analyzed changes in the gut microbiome and its key metabolite short-chain fatty acids (SCFAs). Results indicated that exposure to florfenicol caused gut microbiota dysbiosis, inhibited the production of intestinal SCFAs, and ultimately affected the downstream signaling pathways of SCFA involved in glucose metabolism. Moreover, non-targeted metabolomics revealed that arachidonic acid and linoleic acid metabolic pathways may be associated with insulin sensitivity changes in florfenicol-exposed livers. Overall, this study highlighted a crucial aspect of the environmental risks of florfenicol to both non-target organisms and humans, and presented novel insights into the mechanistic elucidation of metabolic toxicity of antibiotics.

A Well-Established Gut Microbiota Enhances the Efficiency of Nutrient Metabolism and Improves the Growth Performance of Trachinotus ovatus

The gut microbiota has become an essential component of the host organism and plays a crucial role in the host immune system, metabolism, and physiology. Nevertheless, our comprehension of how the fish gut microbiota contributes to enhancing nutrient utilization in the diet and improving host growth performance remains unclear. In this study, we employed a comprehensive analysis of the microbiome, metabolome, and transcriptome to analyze intestines of the normal control group and the antibiotic-treated model group of T. ovatus to investigate how the gut microbiota enhances fish growth performance and uncover the underlying mechanisms. First, we found that the growth performance of the control group was significantly higher than that of the antibiotic-treated model under the same feeding conditions. Subsequent multiomics analyses showed that the gut microbiota can improve its own composition by mediating the colonization of some probiotics represented by Lactobacillus in the intestine, improving host metabolic efficiency with proteins and lipids, and also influencing the expression of genes in signaling pathways related to cell proliferation, which together contribute to the improved growth performance of T. ovatus. Our results demonstrated the important contribution of gut microbiota and its underlying molecular mechanisms on the growth performance of T. ovatus.

Exploring the Dynamic Relationship between the Gut Microbiome and Body Composition across the Human Lifespan: A Systematic Review

This systematic review aimed to identify different gut microbiome profiles across the human lifespan and to correlate such profiles with the body composition. PubMed, Scopus, and Cochrane were searched from inception to March 2022. Sixty studies were included in this systematic review. Overall, the gut microbiome composition in overweight participants exhibited decreased α-diversity, decreased levels of the phylum Bacteroidetes and its taxa, and increased levels of the phylum Firmicutes, its taxa, and the Firmicutes/Bacteroidetes ratio, in comparison to normal-weight participants. Other body composition parameters showed similar correlations. Fat mass and waist circumference were found to correlate positively with the Firmicutes taxa and negatively with the Bacteroidetes taxa. In contrast, lean body mass and muscle mass demonstrated a positive correlation with the Bacteroidetes taxa. Notably, these correlations were more pronounced in athletes than in obese and normal-weight individuals. The composition of the gut microbiome is evidently different in overweight individuals or athletes of all age groups, with the former tending towards decreased Bacteroidetes taxa and increased Firmicutes taxa, while a reversed relationship is observed concerning athletes. Further studies are needed to explore the dynamic relationship between energy intake, body composition, and the gut microbiome across the human lifespan.

Dietary pulses as a means to improve the gut microbiome, inflammation, and appetite control in obesity

A dysbiotic intestinal microbiome has been linked to chronic diseases such as obesity, which may suggest that interventions that target the microbiome may be useful in treating obesity and its complications. Appetite dysregulation and chronic systemic low-grade inflammation, such as that observed in obesity, are possibly linked with the intestinal microbiome and are potential therapeutic targets for the treatment of obesity via the microbiome. Dietary pulses (e.g., common beans) are composed of nutrients and compounds that possess the potential to modulate the gut microbiota composition and function which can in turn improve appetite regulation and chronic inflammation in obesity. This narrative review summarizes the current state of knowledge regarding the connection between the gut microbiome and obesity, appetite regulation, and systemic and adipose tissue inflammation. More specifically, it highlights the efficacy of interventions employing dietary common beans as a means to improve gut microbiota composition and/or function, appetite regulation, and inflammation in both rodent obesity and in humans. Collectively, results presented and discussed herein provide insight on the gaps in knowledge necessary for a comprehensive understanding of the potential of beans as a treatment for obesity while highlighting what further research is required to gain this understanding.

Gut Microbiota and Adipose Tissue Microenvironment Interactions in Obesity

Obesity is an increasingly serious global health problem. Some studies have revealed that the gut microbiota and its metabolites make important contributions to the onset of obesity. The gut microbiota is a dynamic ecosystem composed of diverse microbial communities with key regulatory functions in host metabolism and energy balance. Disruption of the gut microbiota can result in obesity, a chronic metabolic condition characterized by the excessive accumulation of adipose tissue. Host tissues (e.g., adipose, intestinal epithelial, and muscle tissues) can modulate the gut microbiota via microenvironmental interactions that involve hormone and cytokine secretion, changes in nutrient availability, and modifications of the gut environment. The interactions between host tissues and the gut microbiota are complex and bidirectional, with important effects on host health and obesity. This review provides a comprehensive summary of gut microbiota changes associated with obesity, the functional roles of gut microbiota-derived metabolites, and the importance of the complex interactions between the gut microbiota and target tissues in the pathogenesis of obesity. It places particular emphasis on the roles of adipose tissue microenvironment interactions in the onset of obesity.

Beneficial effects of seaweed-derived components on metabolic syndrome via gut microbiota modulation

Metabolic syndrome comprises a group of conditions that collectively increase the risk of abdominal obesity, diabetes, atherosclerosis, cardiovascular diseases, and cancer. Gut microbiota is involved in the pathogenesis of metabolic syndrome, and microbial diversity and function are strongly affected by diet. In recent years, epidemiological evidence has shown that the dietary intake of seaweed can prevent metabolic syndrome via gut microbiota modulation. In this review, we summarize the current in vivo studies that have reported the prevention and treatment of metabolic syndrome via seaweed-derived components by regulating the gut microbiota and the production of short-chain fatty acids. Among the surveyed related articles, animal studies revealed that these bioactive components mainly modulate the gut microbiota by reversing the Firmicutes/Bacteroidetes ratio, increasing the relative abundance of beneficial bacteria, such as Bacteroides, Akkermansia, Lactobacillus, or decreasing the abundance of harmful bacteria, such as Lachnospiraceae, Desulfovibrio, Lachnoclostridium. The regulated microbiota is thought to affect host health by improving gut barrier functions, reducing LPS-induced inflammation or oxidative stress, and increasing bile acid production. Furthermore, these compounds increase the production of short-chain fatty acids and influence glucose and lipid metabolism. Thus, the interaction between the gut microbiota and seaweed-derived bioactive components plays a critical regulatory role in human health, and these compounds have the potential to be used for drug development. However, further animal studies and human clinical trials are required to confirm the functional roles and mechanisms of these components in balancing the gut microbiota and managing host health.

Lactobacillus acidophilus (LA) Fermenting Astragalus Polysaccharides (APS) Improves Calcium Absorption and Osteoporosis by Altering Gut Microbiota

Lactobacillus acidophilus (LA) and Astragalus polysaccharides (APS) have each been shown to have anti-osteoporotic activity, and the aim of this study was to further investigate whether the LA fermenting APS was more effective in improving calcium absorption and osteoporosis than the unfermented mixed solution (MS). We found that the fermentation solution (FS) intervention improved the calcium absorption, BMD, and bone microarchitecture in osteoporotic rats and resulted in better inhibition of osteoclast differentiation markers ACP-5 and pro-inflammatory cytokines TNF-α and IL-6 and promotion of osteoblast differentiation marker OCN. This better performance may be due to the improved restoration of the relative abundance of specific bacteria associated with improved calcium absorption and osteoporosis such as Lactobacillus, Allobaculum, and UCG-005. Several key metabolites, including indicaxanthin, chlorogenic acid, and 3-hydroxymelatonin, may also be the key to the better improvement. In conclusion, the LA fermenting APS can better improve calcium absorption and osteoporosis by increasing active metabolites and altering gut microbiota. This finding should become a solid foundation for the development of LA fermenting APS in functional foods.

The Effect of Gut Microbiota and Probiotics on Metabolism in Fish and Shrimp

The present paper presents an overview of the effects of gut microbiota and probiotics on lipid-, carbohydrate-, protein- and amino acid metabolism in fish and shrimp. In probiotic fish studies, the zebrafish (Danio rerio) model is the most frequently used, and probiotic administration reveals the effect on glucose homeostasis, anti-lipidemic effects and increasing short-chain fatty acids, and increased expressions of genes related to carbohydrate metabolism and innate immunity, along with down-regulation of oxidative stress-related genes. Further, improved length of the intestinal villi and expression of nutrient transporters in fish owing to probiotics exposure have been documented. The present review will present an appraisal of the effect of intestinal microbiota and probiotic administration on the metabolism of nutrients and metabolites related to stress and immunity in diverse fish- and shrimp species. Furthermore, to give the reader satisfactory information on the topics discussed, some information from endothermic animals is also presented.

Shifts in the intestinal microflora of meat rabbits in response to glucocorticoids

BACKGROUND

As major stress hormones, glucocorticoids can directly or indirectly affect the intestinal microflora, although few studies have focused on changes in the composition of the intestinal microflora. In this study, rabbits were randomly divided into two groups: gavage administration with saline, and the same doses of dexamethasone (1 mg kg^-1 ). After 7 days, the microbial diversity of the jejunum contents was analysed.

RESULTS

The gut microflora richness and diversity had no significant difference between the two groups. The proportions of Firmicutes and Bacteroidetes were the most abundant in the jejunum of meat rabbits. Dexamethasone injection led to a change in the structure of the gut microflora composition, and we found that there were six biomarkers with linear discriminant analysis score >4 (Firmicutes, Caproiciproducens, Clostridiales, Clostridia, Psychrobacter, and Psychrobacter faecalis), moreover, the results of this study provide new insight into alleviating the effects of stress on meat rabbits.

CONCLUSION

It was concluded that glucocorticoids caused changes in the composition of intestinal microflora. © 2022 Society of Chemical Industry.

Insights into the proteomic profile of newly harvested corn and metagenomic analysis of the broiler intestinal microbiota

Background

The use of newly harvested corn in feed causes wet droppings in broilers and increased feed cost which was termed as “new season grain problem”. The present study was conducted to evaluate the proteomic profile of newly harvested corn and the subsequent influence on intestinal microbiol community for broiler chickens.

Methods

Newly harvested corn stored for either half a month (HM) or two months (TM) was used, and the pasting properties, total soluble sugars, and proteomic analysis technology was used to explore the influence of storage on natural aging corn properties. Additionally, seventy-two 7-day-old Ross 308 male broiler chicken were fed with different stored corn. Apparent metabolizable energy (AME), digesta viscosity, intestinal morphology and microbiota were examined to explore the influence of feed corn storage on broiler chickens.

Results

Pasting properties in the TM corn exhibited decreased viscoelastic properties. Proteomic studies found a total of 26 proteins that were differentially expressed between the two treatment groups. Proteins involved in starch and polysaccharides biosynthesis were upregulated in TM compared with HM. Chickens fed on TM diet had higher relative energy utilization compared to the HM birds. With increased corn storage, the relative digesta viscosity decreased significantly (P ≤ 0.05). The total number of goblet cells and lymphocytes was lower in chickens fed the TM diet. The microbiota data showed that the TM chickens had decreased abundance of diarrheal bacteria such as Hungatella hathewayi and Bacteroides fragilis, and increased butyrate-producing bacteria such as Alistipes compared to the HM chickens.

Conclusions

Storage of newly harvested corn induced the synthetic reaction of large molecules and changed the solubility of starch and protein with increasing soluble sugars and decreasing pasting properties that may improve the fermentation of intestinal microbiota, improve the energy utilization and protect gut health without the risk of diarrhea.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00656-1.

Diet-induced obesity leads to alterations in behavior and gut microbiota composition in mice

The high prevalence of obesity and associated metabolic disorders are one of the major public health problems worldwide. Among the main causal factors of obesity, excessive consumption of food rich in sugar and fat stands out due to its high energy density. The regulation of food intake relies on hypothalamic control by the action of several neuropeptides. Excessive consumption of hypercaloric diets has impact in the behavior and in the gut microbiota. In the present study, we used a high-sugar and fat (HSB) diet for 12 weeks to induce obesity in C57BL/6 mice and to investigate its effects on the gut microbiota, hypothalamic peptides, and behavior. We hypothesize that chronic consumption of HSB diet can change the behavior. Additionally, we also hypothesize that changes in gut microbiota can be associated with changes in the transcriptional regulation of hypothalamic peptides and behavior. To evaluate the gut microbiota, we performed the sequencing of 16S rRNA gene, which demonstrate that HSB diet modulates the gut microbiota with an increase in the Firmicutes and Actinobacteria phylum and a decrease of Bacteroidetes phylum. The real time qPCR revealed that HSB-fed mice presented changes in the transcriptional regulation of hypothalamic neuropeptides genes such as Npy, Gal and Galr1. The Marble-burying and Light/dark box tests also showed an alteration in anxiety and impulsive behaviors for the HSB-fed mice. Our data provides evidence that obesity induced by HSB diet consumption is associated with alterations in gut microbiota and behavior, highlighting the multifactorial characteristics of this disease.

Gut microbiome responses in the metabolism of human dietary components: Implications in health and homeostasis

The gut microbiome and its link with human health and disease have gained a lot of attention recently. The microbiome executes its functions in the host by carrying out the transformation of dietary components and/or de novo synthesis of various essential nutrients. The presence of complex microbial communities makes it difficult to understand the host-microbiome interplay in the metabolism of dietary components. This review attempts to uncover the incredible role of the gut microbiome in the metabolism of dietary components, diet-microbiome interplay, and restoration of the microbiome. The in silico analysis performed in this study elucidates the functional description of essential/hub genes involved in the amino acid degradation pathway, which are mutually present in the host and its gut microbiome. Hence, the computational model helps comprehend the inter-and intracellular molecular networks between humans and their microbial partners.

Effects of Anthocyanin on Intestinal Health: A Systematic Review

Intestinal health relies on the association between the mucosal immune system, intestinal barrier and gut microbiota. Bioactive components that affect the gut microbiota composition, epithelial physical barrier and intestinal morphology were previously studied. The current systematic review evaluated evidence of anthocyanin effects and the ability to improve gut microbiota composition, their metabolites and parameters of the physical barrier; this was conducted in order to answer the question: "Does food source or extract of anthocyanin promote changes on intestinal parameters?". The data analysis was conducted following the PRISMA guidelines with the search performed at PubMed, Cochrane and Scopus databases for experimental studies, and the risk of bias was assessed by the SYRCLE tool. Twenty-seven studies performed in animal models were included, and evaluated for limitations in heterogeneity, methodologies, absence of information regarding allocation process and investigators' blinding. The data were analyzed, and the anthocyanin supplementation demonstrated positive effects on intestinal health. The main results identified were an increase of Bacteroidetes and a decrease of Firmicutes, an increase of short chain fatty acids production, a decrease of intestinal pH and intestinal permeability, an increase of the number of goblet cells and tight junction proteins and villi improvement in length or height. Thus, the anthocyanin supplementation has a potential effect to improve the intestinal health. PROSPERO (CRD42020204835).

Mutual interaction between gut microbiota and protein/amino acid metabolism for host mucosal immunity and health

In recent years, many studies have shown that the intestinal microflora has various effects that are linked to the critical physiological functions and pathological systems of the host. The intestinal microbial community is widely involved in the metabolism of food components such as protein, which is one of the essential nutrients in diets. Additionally, dietary protein/amino acids have been shown to have had a profound impact on profile and operation of gut microbiota. This review summarizes the current literature on the mutual interaction between intestinal microbiota and protein/amino acid metabolism for host mucosal immunity and health.

Effect of Duyun Compound Green Tea on Gut Microbiota Diversity in High-Fat-Diet-Induced Mice Revealed by Illumina High-Throughput Sequencing

Intake of a high-fat diet (HFD) is closely related to disorders of the intestinal microbiota, which plays a key role in the pathogenesis of obesity. Duyun compound green tea, an ancient Chinese drink, is widely consumed to reduce weight, although the mechanism is not clear. In this study, 50 mice were randomly divided into 5 groups: normal control group (CK), HFD model control group (NK), positive control group with medicine (YK), low-dose compound tea group (DL), and high-dose compound tea group (DH). After 4 weeks of intervention, the feces of mice were taken under sterile conditions and evaluated using Illumina high-throughput sequencing technology. The results showed that the diversity of intestinal microbiota was the highest in the CK group, the lowest in the NK group, and relatively increased in the compound tea treatment group. Second, there were differences in intestinal microbiota in each group, among which the beneficial bacteria in the intestinal tract of the CK group were higher than those in the other groups, while the beneficial bacteria in each compound tea treatment group were more abundant than those in the NK group, in which harmful bacteria in the intestinal tract were found to be the highest. These results suggest that compounds in tea may be able to attenuate imbalances of intestinal microbiota induced by poor diet, acting as a therapeutic agent in obesity or other diseases associated with gut dysbiosis.

Ruminal microbiota-host interaction and its effect on nutrient metabolism

Rumen microbiota has a close and intensive interaction with the ruminants. Microbiota residing in the rumen digests and ferments plant organic matters into nutrients that are subsequently utilized by the host, making ruminants a unique group of animals that can convert plant materials indigestible by humans into high-quality animal protein as meat and milk. Many studies using meta-omics technologies have demonstrated the relationships between rumen microbiome and animal phenotypes associated with nutrient metabolism. Recently, the causality and physiological mechanisms underpinning the host-microbiota interactions have attracted tremendous research interest among researchers. This review discusses the host-microbiota interactions and the factors affecting these interactions in ruminants and provides a summary of the advances in research on animal husbandry. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to enhance animal productivity and host health.

Compound Fu brick tea modifies the intestinal microbiome composition in high-fat diet-induced obesity mice

Compound Fu Brick Tea (CFBT), which is from Duyun city in China, is a traditional Chinese dark tea, Fu Brick Tea, mixed with six herbal medicine. It is consumed by local people for reducing weight, but the mechanism is not clear. The disorder of intestinal microbiome caused by long-term high-fat diet (HFD) is one of the inducements of obesity and related metabolic syndrome. In this study, mice were fed with HFD to establish a high-fat model. Fifty mice were randomly divided into six groups: normal control (CK), HFD model control (NK), positive control with medicine (YK), CFBT groups with low, middle, and high dose (FL, FM, FH). The V3-V4 DNA region of fecal microbiome from mouse intestine was sequenced. The results showed that the diversity of intestinal microflora was highest in CK and lowest in NK. Compared with CK, the dominant bacterium Firmicutes was increased and Bacteroidetes decreased at phylum level in NK. Compared with NK, the abundance of microbiome in CFBT groups was significantly higher and the composition was changed: Muribaculaceae, Bacteroidaceae, and Prevotellaceae increased and Lachnospiraceae decreased in CFBT groups at family level, while at the genus level, Bacteroides increased and Lactobacillus decreased. These results conclude that CFBT can increase the abundance of intestinal microbiome in mice, promote the growth of beneficial bacteria and reduce the number of pathogenic bacteria, and restore the imbalance of intestinal microbiome caused by poor diet.

Bacterial community evolution along full-scale municipal wastewater treatment processes

Sewage pollution is a major threat to public health because sewage is always accompanied by pathogens. Generally, wastewater treatment plants (WWTP) receive and treat sewage to control pathogenic risks and improve environmental health. This study investigated the changes in the bacterial community over the course of treatment by a WWTP. Illumina MiSeq high-throughput sequencing was performed to characterize the bacterial communities in the WWTP. This study found that potential pathogens in the WWTP, especially the genera Arcobacter and Acinetobacter, were greatly reduced. In addition, high chemical oxygen demand levels provided excessive growth substrates for the genera Hyphomicrobium and Rhodoplanes, the abundance of which could exceed autotrophic bacteria, increasing the ammonium removal. According to the network analysis, the bacterial assemblage was not randomly arranged in the WWTP, and various defined processes led to higher intra-phylum (such as Proteobacteria) coexistence than expected. Moreover, the metabolic functions of bacterial communities significantly improved in the WWTP compared with the influent. Together, the data in this study emphasize the need to understand the bacterial community of WWTPs better. When analyzing the risks of WWTP drainage systems to the environment and human health, these data should be considered.

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.

Evaluating the Impact of Four Major Nutrients on Gut Microbial Metabolism by a Targeted Metabolomics Approach

Gut microbiome plays fundamental roles in host physiology, and gut microbial metabolism is important to the host-microbiome homeostasis. As major contributors to gut microbial metabolism, the medium nutritional components are essential to in vitro gut microbiome growths, and four nutrients, namely, inorganic salts, bile salts, short-chain fatty acids (SCFAs), and mucin, have gained particular attention because of their significant variation found in different growth environments and their ability to modulate the gut microbial population and functions. However, a systematic study is lacking to evaluate the effects of these four nutrients on the gut microbiome in terms of their impact on the microbial metabolic profiles. To fill the gap of the knowledge, we applied mass-spectrometry-based targeted metabolomics approach to study the regulation effects of these four medium components on in vitro-cultured gut microbiota. Our results show that inorganic salts and mucin had the greatest impacts on the gut microbiome metabolic profile compared to the other components studied, with gut microbial cultures grown with low-concentration inorganic salts and mucin-supplemented medium demonstrating greater numbers of metabolites detected. We also applied metabolic pathway impact analysis, which revealed several significantly impacted metabolic pathways during the comparison of different medium supplements, which could further assist our understanding of the overall impacts of certain critical nutrients on gut microbial metabolism. In summary, this pilot study can serve as a first attempt to evaluate the individual nutritional component in their contribution to gut microbial metabolic functions.

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota

The human gut microbiome impacts several aspects of human health and disease, including digestion, drug metabolism and the propensity to develop various inflammatory, autoimmune and metabolic diseases. Many of the molecular processes that play a role in the activity and dynamics of the microbiota go beyond species and genic composition and thus, their understanding requires advanced bioinformatics support. This article aims to provide an up-to-date view of the resources and software tools that are being developed and used in human gut microbiome research, in particular data integration and systems-level analysis efforts. These efforts demonstrate the power of standardized and reproducible computational workflows for integrating and analysing varied omics data and gaining deeper insights into microbe community structure and function as well as host-microbe interactions.

Profile of the gut microbiota of adults with obesity: a systematic review

Recently, relationship between gut microbiota composition and development of obesity has been pointed. However, the gut microbiota composition of individual with obesity is not known yet. Therefore, this systematic review aimed to evaluate differences in profile of gut microbiota between individuals with obesity and individuals with normal weight. A search performed on August 2019 in the databases Pubmed, Scopus, Web of Science, Cochrane library, Lilacs and gray literature using the terms: "microbiota", "microbiome", "obesity", "obesity morbid", and "humans". Studies assessing the gut microbiota composition in adults with obesity and lean were included. Quality assessment was performed by Newcastle-Ottawa Quality Assessment Scale. Of the 12,496 studies, 32 were eligible and included in this review. Individuals with obesity have a greater Firmicutes/Bacteroidetes ratio, Firmicutes, Fusobacteria, Proteobacteria, Mollicutes, Lactobacillus (reuteri), and less Verrucomicrobia (Akkermansia muciniphila), Faecalibacterium (prausnitzii), Bacteroidetes, Methanobrevibacter smithii, Lactobacillus plantarum and paracasei. In addition, some bacteria had positive correlation and others negative correlation with obesity. Individuals with obesity showed profile of gut microbiota different than individual lean. These results may help in advances of the diagnosis and treatment of obesity.

Pharmacomicrobiomics: The Holy Grail to Variability in Drug Response?

The human body, with 3.0 × 10¹³ cells and more than 3.8 × 10¹³ microorganisms, has nearly a one-to-one ratio of resident microbes to human cells. Initiatives like the Human Microbiome Project, American Gut, and Flemish Gut have identified associations between microbial taxa and human health. The study of interactions between microbiome and pharmaceutical agents, i.e., pharmacomicrobiomics, has revealed an instrumental role of the microbiome in modulating drug response that alters the therapeutic outcomes. In this review, we present our current comprehension of the relationship of the microbiome, host biology, and pharmaceutical agents such as cardiovascular drugs, analgesics, and chemotherapeutic agents to human disease and treatment outcomes. We also discuss the significance of studying diet-gene-drug interactions and further address the key challenges associated with pharmacomicrobiomics. Finally, we examine proposed models employing systems biology for the application of pharmacomicrobiomics and other -omics data, and provide approaches to elucidate microbiome-drug interactions to improve future translation to personalized medicine.

Drug pharmacomicrobiomics and toxicomicrobiomics: from scattered reports to systematic studies of drug-microbiome interactions

INTRODUCTION

Pharmacomicrobiomics and toxicomicrobiomics study how variations within the human microbiome (the combination of human-associated microbial communities and their genomes) affect drug disposition, action, and toxicity. These emerging fields, interconnecting microbiology, bioinformatics, systems pharmacology, and toxicology, complement pharmacogenomics and toxicogenomics, expanding the scope of precision medicine. Areas covered: This article reviews some of the most recently reported pharmacomicrobiomic and toxicomicrobiomic interactions. Examples include the impact of the human gut microbiota on cardiovascular drugs, natural products, and chemotherapeutic agents, including immune checkpoint inhibitors. Although the gut microbiota has been the most extensively studied, some key drug-microbiome interactions involve vaginal, intratumoral, and environmental bacteria, and are briefly discussed here. Additionally, computational resources, moving the field from cataloging to predicting interactions, are introduced. Expert opinion: The rapid pace of discovery triggered by the Human Microbiome Project is moving pharmacomicrobiomic research from scattered observations to systematic studies focusing on screening microbiome variants against different drug classes. Better representation of all human populations will improve such studies by avoiding sampling bias, and the integration of multiomic studies with designed experiments will allow establishing causation. In the near future, pharmacomicrobiomic testing is expected to be a key step in screening novel drugs and designing precision therapeutics.

Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota

Microbial communities thrive in a number of environments. Exploration of their microbiomes – their global genome – may reveal metabolic features that contribute to the development and welfare of their hosts, or chemical cleansing of environments. Yet we often lack final demonstration of their causal role in features of interest. The reason is that we do not have proper baselines that we could use to monitor how microbiota cope with key metabolites in the hosting environment. Here, focusing on animal gut microbiota, we describe the fate of cobalamins – metabolites of the B12 coenzyme family – that are essential for animals but synthesized only by prokaryotes. Microbiota produce the vitamin used in a variety of animals (and in algae). Coprophagy plays a role in its management. For coprophobic man, preliminary observations suggest that the gut microbial production of vitamin B12 plays only a limited role. By contrast, the vitamin is key for structuring microbiota. This implies that it is freely available in the environment. This can only result from lysis of the microbes that make it. A consequence for biotechnology applications is that, if valuable for their host, B12‐producing microbes should be sensitive to bacteriophages and colicins, or make spores.

Mechanisms of cross-talk between the diet, the intestinal microbiome, and the undernourished host

Undernutrition remains one of the most pressing global health challenges today, contributing to nearly half of all deaths in children under five years of age. Although insufficient dietary intake and environmental enteric dysfunction are often inciting factors, evidence now suggests that unhealthy gut microbial populations perpetuate the vicious cycle of pathophysiology that results in persistent growth impairment in children. The metagenomics era has facilitated new research identifying an altered microbiome in undernourished hosts and has provided insight into a number of mechanisms by which these alterations may affect growth. This article summarizes a range of observational studies that highlight differences in the composition and function of gut microbiota between undernourished and healthy children; discusses dietary, environmental and host factors that shape this altered microbiome; examines the consequences of these changes on host physiology; and considers opportunities for microbiome-targeting therapies to combat the global challenge of child undernutrition.

Probiotics, gut microbiota, and their influence on host health and disease

The gastrointestinal tract of mammals hosts a high and diverse number of different microorganisms, known as intestinal microbiota. Many probiotics were originally isolated from the gastrointestinal tract, and they were defined by the Food and Agriculture Organization of the United Nations (FAO)/WHO as "live microorganisms which when administered in adequate amounts confer a health benefit on the host." Probiotics exert their beneficial effects on the host through four main mechanisms: interference with potential pathogens, improvement of barrier function, immunomodulation and production of neurotransmitters, and their host targets vary from the resident microbiota to cellular components of the gut-brain axis. However, in spite of the wide array of beneficial mechanisms deployed by probiotic bacteria, relatively few effects have been supported by clinical data. In this regard, different probiotic strains have been effective in antibiotic-associated diarrhea or inflammatory bowel disease for instance. The aim of this review was to compile the molecular mechanisms underlying the beneficial effects of probiotics, mainly through their interaction with the intestinal microbiota and with the intestinal mucosa. The specific benefits discussed in this paper include among others those elicited directly through dietary modulation of the human gut microbiota.

Analysis of the intestinal microbial community and inferred functional capacities during the host response to Pneumocystis pneumonia

BACKGROUND

Pneumocystis pneumonia is a major cause of morbidity and mortality in patients infected with HIV/AIDS. In this study, we evaluated the intestinal microbial communities associated with the development of experimental Pneumocystis pneumonia, as there is growing evidence that the intestinal microbiota is critical for host defense against fungal pathogens.

METHODS

C57BL/6 mice were infected with live Pneumocystis murina (P. murina) via intratracheal inoculation and sacrificed 7 and 14 days postinfection for microbiota analysis. In addition, we evaluated the intestinal microbiota from CD4+ T cell depleted mice infected with P. murina.

RESULTS

We found that the diversity of the intestinal microbial community was significantly altered by respiratory infection with P. murina. Specifically, mice infected with P. murina had altered microbial populations, as judged by changes in diversity metrics and relative taxa abundances. We also found that CD4+ T cell depleted mice infected with P. murina exhibited significantly altered intestinal microbiota that was distinct from immunocompetent mice infected with P. murina, suggesting that loss of CD4+ T cells may also affects the intestinal microbiota in the setting of Pneumocystis pneumonia. Finally, we employed a predictive metagenomics approach to evaluate various microbial features. We found that Pneumocystis pneumonia significantly alters the intestinal microbiota's inferred functional potential for carbohydrate, energy, and xenobiotic metabolism, as well as signal transduction pathways.

CONCLUSIONS

Our study provides insight into specific-microbial clades and inferred microbial functional pathways associated with Pneumocystis pneumonia. Our data also suggest a role for the gut-lung axis in host defense in the lung.

Impact of macronutrients on gut microbiota

The human gastrointestinal tract is colonized by microbial communities that have important effects on immune function, nutrient processing, and a broad range of other host activities. Diet and other environmental factors can modulate the composition and metabolic activity of the gut microbiota, which in turn impacts health. On the other hand, microbiota and its collective genomes provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest nutrients such as polysaccharides. This review will focus on the impact of dietary macronutrients (carbohydrate, protein and fat) on the microbial ecology and metabolism within the intestine, and explore some of the consequences for animal health.

Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology?

INTRODUCTION

Our microbiome harbours a metabolic capacity far beyond our own. Moreover, its gene pool is highly adaptable and subject to selective pressure, including host exposure to xenobiotics. Yet, the resulting adaptations do not necessarily follow host well-being and can therefore contribute to disease or unfavourable metabolite production.

AREAS COVERED

This review provides an overview of our host-microbiome relationship in light of bacterial (xenobiotic) metabolism, community dynamics, entero-endocrine crosstalk, dysbiosis and potential therapeutic targets. In addition, it will highlight the need for a systematic analysis of the microbiome's potential for substance toxification.

EXPERT OPINION

The influence of our microbiota reaches from primary metabolites to secondary effects such as substrate competition or the activation of eukaryotic Phase I and Phase II enzymes. Further on it plays a hitherto underestimated role in drug metabolism, toxicity and pathogenesis. These effects are partly caused by entero-endocrine crosstalk and interference with eukaryotic regulatory networks. On first sight, the resulting concept of a metabolically competent microbiome adds enormous complexity to human physiology. Yet, the potential specificity of microbial targets harbours therapeutic promise for diseases such as diabetes, cancer and psychiatric disorders. A better physiological and biochemical understanding of the microbiome is thus of high priority for academia and biomedical research.

Rational identification of diet-derived postbiotics for improving intestinal microbiota function

The intestinal microbiota plays an important role in a wide range of functions and whole body homeostasis. Recent advances have linked microbiota dysbiosis to conditions ranging from Crohn's disease to cancer. The restoration or strengthening of the intestinal microbiota through diet-based approaches such as probiotics and prebiotics has been proposed for combating the onset or progression of these diseases. In this review, we highlight the importance of postbiotics for the manipulation of the intestinal microbiota, with special emphasis on systems biology computational tools and targeted metabolomics for the rational discovery and identification of these bioactive molecules. The identification of novel postbiotics and the pathways responsible for their production should lead to improved mechanistic understanding of the role that specific probiotics, prebiotics, and postbiotics have in restoring intestinal microbiota composition and function.

Interwoven biology of the tsetse holobiont

Microbial symbionts can be instrumental to the evolutionary success of their hosts. Here, we discuss medically significant tsetse flies (Diptera: Glossinidae), a group comprised of over 30 species, and their use as a valuable model system to study the evolution of the holobiont (i.e., the host and associated microbes). We first describe the tsetse microbiota, which, despite its simplicity, harbors a diverse range of associations. The maternally transmitted microbes consistently include two Gammaproteobacteria, the obligate mutualists Wigglesworthia spp. and the commensal Sodalis glossinidius, along with the parasitic Alphaproteobacteria Wolbachia. These associations differ in their establishment times, making them unique and distinct from previously characterized symbioses, where multiple microbial partners have associated with their host for a significant portion of its evolution. We then expand into discussing the functional roles and intracommunity dynamics within this holobiont, which enhances our understanding of tsetse biology to encompass the vital functions and interactions of the microbial community. Potential disturbances influencing the tsetse microbiome, including salivary gland hypertrophy virus and trypanosome infections, are highlighted. While previous studies have described evolutionary consequences of host association for symbionts, the initial steps facilitating their incorporation into a holobiont and integration of partner biology have only begun to be explored. Research on the tsetse holobiont will contribute to the understanding of how microbial metabolic integration and interdependency initially may develop within hosts, elucidating mechanisms driving adaptations leading to cooperation and coresidence within the microbial community. Lastly, increased knowledge of the tsetse holobiont may also contribute to generating novel African trypanosomiasis disease control strategies.

Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes

The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based phylogeny and metagenomics. Following the completion of the Human Genome Project, the rapid, substantial growth of the Human Microbiome Project (HMP) opens new horizons for studying how microbiome compositional and functional variations affect drug action, fate, and toxicity (pharmacomicrobiomics), notably in the human gut. The HMP continues to characterize the microbial communities associated with the human gut, determine whether there is a common gut microbiome profile shared among healthy humans, and investigate the effect of its alterations on health. Here, we offer a glimpse into the known effects of the gut microbiota on xenobiotic metabolism, with emphasis on cases where microbiome variations lead to different therapeutic outcomes. We discuss a few examples representing how the microbiome interacts with human metabolic enzymes in the liver and intestine. In addition, we attempt to envisage a roadmap for the future implications of the HMP on therapeutics and personalized medicine.