Gut Bacterial Community Structure Research Articles

Obesity and Asthma: Microbiome-Metabolome Interactions.

Obesity is a risk factor for asthma, but obese subjects with asthma respond poorly to standard asthma drugs. Obesity also alters gut bacterial community structure. Obesity-related changes in gut bacteria contribute to weight gain and other obesity-related conditions, including insulin resistance and systemic inflammation. Here, we review the rationale for the hypothesis that obesity-related changes in gut bacteria may also play a role in obesity-related asthma. The metabolomes of the liver, serum, urine, and adipose tissue are altered in obesity. Gut bacteria produce a large number of metabolites, which can reach the blood and circulate to other organs, and gut bacteria-derived metabolites have been shown to contribute to disease processes outside the gastrointestinal tract, including cardiovascular disease. Here, we describe the potential roles for two such classes of metabolites in obesity-related asthma: short-chain fatty acids and bile acids. Greater understanding of the role of microbiota in obesity-related asthma could lead to novel microbiota-based treatments for these hard-to-treat patients.

A polyphenol-rich fraction obtained from table grapes decreases adiposity, insulin resistance and markers of inflammation and impacts gut microbiota in high-fat-fed mice

The objective of this study was to determine if consuming an extractable or nonextractable fraction of table grapes reduced the metabolic consequences of consuming a high-fat, American-type diet. Male C57BL/6J mice were fed a low fat (LF) diet, a high fat (HF) diet, or an HF diet containing whole table grape powder (5% w/w), an extractable, polyphenol-rich (HF-EP) fraction, a nonextractable, polyphenol-poor (HF-NEP) fraction or equal combinations of both fractions (HF-EP+NEP) from grape powder for 16weeks. Mice fed the HF-EP and HF-EP+NEP diets had lower percentages of body fat and amounts of white adipose tissue (WAT) and improved glucose tolerance compared to the HF-fed controls. Mice fed the HF-EP+NEP diet had lower liver weights and triglyceride (TG) levels compared to the HF-fed controls. Mice fed the HF-EP+NEP diets had higher hepatic mRNA levels of hormone sensitive lipase and adipose TG lipase, and decreased expression of c-reactive protein compared to the HF-fed controls. In epididymal (visceral) WAT, the expression levels of several inflammatory genes were lower in mice fed the HF-EP and HF-EP+NEP diets compared to the HF-fed controls. Mice fed the HF diets had increased myeloperoxidase activity and impaired localization of the tight junction protein zonula occludens-1 in ileal mucosa compared to the HF-EP and HF-NEP diets. Several of these treatment effects were associated with alterations in gut bacterial community structure. Collectively, these data demonstrate that the polyphenol-rich, EP fraction from table grapes attenuated many of the adverse health consequences associated with consuming an HF diet.

Fecal bacterial community changes associated with isoflavone metabolites in postmenopausal women after soy bar consumption.

Soy isoflavones and their metabolism by intestinal microbiota have gained attention because of potential health benefits, such as the alleviation of estrogen/hormone-related conditions in postmenopausal women, associated with some of these compounds. However, overall changes in gut bacterial community structure and composition in response to addition of soy isoflavones to diets and their association with excreted isoflavone metabolites in postmenopausal women has not been studied. The aim of this study was to determine fecal bacterial community changes in 17 postmenopausal women after a week of diet supplementation with soy bars containing isoflavones, and to determine correlations between microbial community changes and excreted isoflavone metabolites. Using DGGE profiles of PCR amplified 16S rRNA genes (V3 region) to compare microbial communities in fecal samples collected one week before and one week during soy supplementation revealed significant differences (ANOSIM p<0.03) before and after soy supplementation in all subjects. However, between subjects comparisons showed high inter-individual variation that resulted in clustering of profiles by subjects. Urinary excretion of isoflavone (daidzein) metabolites indicated four subjects were equol producers and all subjects produced O-desmethylangolensin (ODMA). Comparison of relative proportions of 16S rRNA genes from 454 pyrosequencing of the last fecal samples of each treatment session revealed significant increases in average proportions of Bifidobacterium after soy consumption, and Bifidobacterium and Eubacterium were significantly greater in equol vs non-S-(-)equol producers. This is the first in vivo study using pyrosequencing to characterize significant differences in fecal community structure and composition in postmenopausal women after a week of soy diet-supplementation, and relate these changes to differences in soy isoflavones and isoflavone metabolites.Trial RegistrationClinicaltrials.gov NCT00244907

16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species)

The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.) using 16S rRNA gene sequencing of clone libraries. Clone libraries were screened by restriction fragment length polymorphism and representative clones from O. somaliensis (100 out of 330 clones), Odontotermes sp. (100 out of 359 clones) and Microtermes sp. (96 out 336 clones) were sequenced. Phylogenetic analysis indicated seven bacterial phyla were represented: Bacteroidetes, Spirochaetes, Firmicutes, Proteobacteria, Synergistetes, Planctomycetes and Actinobacteria. Sequences representing the phylum Bacteroidetes (>60%) were the most abundant group in Odontotermes while those of Spirochaetes (29%) and Firmicutes (23%) were the abundant groups in Microtermes. The gut bacterial community structure within the two Odontotermes species investigated here was almost identical at the phylum level, but the Microtermes sp. had a unique bacterial community structure. Bacterial diversity was higher in Odontotermes than in Microtermes. The affiliation and clustering of the sequences, often with those from other termites' guts, indicate a majority of the gut bacteria are autochthonous having mutualistic relationships with their hosts. The findings underscore the presence of termite-specific bacterial lineages, the majority of which are still uncultured.

Host species as a strong determinant of the intestinal microbiota of fish larvae

We investigated the influence of host species on intestinal microbiota by comparing the gut bacterial community structure of four cohabitating freshwater fish larvae, silver carp, grass carp, bighead carp, and blunt snout bream, using denaturing gradient gel electrophoresis (DGGE) of the amplified 16S and 18S rRNA genes. Similarity clustering indicated that the intestinal microbiota derived from these four fish species could be divided into four groups based on 16S rRNA gene similarity, whereas the eukaryotic 18S rRNA genes showed no distinct groups. The water sample from the shared environment contained microbiota of an independent group as indicated by both 16S and 18S rRNA genes segments. The bacterial community structures were visualized using rank-abundance plots fitted with linear regression models. Results showed that the intestinal bacterial evenness was significantly different between species (P<0.05) and between species and the water sample (P<0.01). Thirty-five relatively dominant bands in DGGE patterns were sequenced and grouped into five major taxa: Proteobacteria (26), Actinobacteria (5), Bacteroidetes (1), Firmicutes (2), and Cyanobacterial (1). Six eukaryotes were detected by sequencing 18S rRNA genes segments. The present study suggests that the intestines of the four fish larvae, although reared in the same environment, contained distinct bacterial populations, while intestinal eukaryotic microorganisms were almost identical.

Denaturing gradient gel electrophoresis analysis of gut bacterial community for the Japanese earthworms

The gut bacterial community structure for Pheretima hilgendorfi and P. heteropoda (Family Megascolecidae), and Allolobophora japonica (Family Lumbricidae) collected from agricultural grasslands in Japan was analyzed by denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S rRNA gene fragments (PCR-DGGE) and compared with those in the surrounding soils. Denaturing gradient gel electrophoresis (DGGE) profiles indicated that each earthworm species had their own specific bacterial communities, and multidimentional scaling analysis grouped the DGGE profiles into three groups: gut samples from P. hilgendorfi and P. heteropoda, gut samples from A. japonica and samples from the surrounding soils. Nine dominant bands were identified by their direct sequencing and cloning. Major three bands from P. hilgendorfi and P. heteropoda were closely related to Bacillus species belonging to the phylum Firmicutes. Major four and two bands from A. japonica were closely related to the phyla Proteobacteria and Bacteroidetes, respectively.

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

Studies in mice indicate that the gut microbiome influences both sides of the energy-balance equation by contributing to nutrient absorption and regulating host genes that affect adiposity. However, it remains uncertain as to what extent gut microbiota are an important regulator of nutrient absorption in humans. With the use of a carefully monitored inpatient study cohort, we tested how gut bacterial community structure is affected by altering the nutrient load in lean and obese individuals and whether their microbiota are correlated with the efficiency of dietary energy harvest. We investigated dynamic changes of gut microbiota during diets that varied in caloric content (2400 compared with 3400 kcal/d) by pyrosequencing bacterial 16S ribosomal RNA (rRNA) genes present in the feces of 12 lean and 9 obese individuals and by measuring ingested and stool calories with the use of bomb calorimetry. The alteration of the nutrient load induced rapid changes in the gut microbiota. These changes were directly correlated with stool energy loss in lean individuals such that a 20% increase in Firmicutes and a corresponding decrease in Bacteroidetes were associated with an increased energy harvest of ≈150 kcal. A high degree of overfeeding in lean individuals was accompanied by a greater fractional decrease in stool energy loss. These results show that the nutrient load is a key variable that can influence the gut (fecal) bacterial community structure over short time scales. Furthermore, the observed associations between gut microbes and nutrient absorption indicate a possible role of the human gut microbiota in the regulation of the nutrient harvest. This trial was registered at clinicaltrials.gov as NCT00414063.

Manipulation of the microbiota of mass-reared Mediterranean fruit flies Ceratitis capitata (Diptera: Tephritidae) improves sterile male sexual performance

The sterile insect technique (SIT) is a method of biological control whereby millions of factory reared sterile male insects are released into the field. This technique is commonly used to combat the Mediterranean fruit fly (Ceratitis capitata, Diptera: Tephritidae). Sterile medfly males are less competent in attracting and mating with wild females, a property commonly linked to the irradiation process responsible for the sterilization. As bacteria are important partners in the fly's life cycle, we used molecular analytical methods to study the community structure of the gut microbiota in irradiated male medflies. We find that the sterilizing irradiation procedure affects the gut bacterial community structure of the Mediterranean fruit fly. Although the Enterobacteriaceae family remains the dominant bacterial group present in the gut, the levels of Klebsiella species decreases significantly in the days after sterilization. In addition, we detected substantial differences in some bacterial species between the mass rearing strain Vienna 8 and the wild strain. Most notable among these are the increased levels of the potentially pathogenic species Pseudomonas in the industrial strain. Testing the hypothesis that regenerating the original microbiota community could result in enhanced competitiveness of the sterile flies, we found that the addition of the bacterial species Klebsiella oxytoca to the postirradiation diet enables colonization of these bacteria in the gut while resulting in decreased levels of the Pseudomonas sp. Feeding on diets containing bacteria significantly improved sterile male performance in copulatory tests. Further studies will determine the feasibility of bacterial amelioration in SIT operations.

Gut bacterial community structure (Porcellio Scaber, Isopoda, Crustacea) as a measure of community level response to long‐term and short‐term metal pollution

Prokaryotes are of high importance in the assessment of environmental pollution effects. Due to fast responsiveness of bacterial communities to environmental physicochemical factors, it is difficult to compare results of bacterial community investigations on the temporal and spatial scale. To reduce the effects of variable physicochemical environmental conditions on bacterial microbiota when investigating the specific impact of contaminants on bacterial communities, we investigated the bacterial community in the gut of terrestrial isopods (Porcellio scaber, Isopoda, Crustacea) from clean and metal-polluted environments. Animals were collected from a chronically mercury-polluted site, a chronically multiple metal-(Cd, Pb, Zn) polluted site, and two reference sites. In addition, animals from an unpolluted site were laboratory exposed to 5 microg Hg/g food in order to compare the effect of acute and chronic Hg exposure. The bacterial gut microbiota was investigated by temporal temperature gradient gel electrophoresis (TTGE) and clone library construction based on polymerase chain reaction amplified 16S rRNA genes. The major bacterial representatives of the emptied gut microbiota in the animals from the chronically polluted environments seemed not affected when analyzed by TTGE. The detailed bacterial community structure investigated by 16S rRNA clone library construction, however, showed that the community from the Hg-polluted site also was affected severely (242.4 operational taxonomic units [OTU] in the polluted and 650.6 OTU in the unpolluted environment). When animals were acutely exposed to mercury, changes of bacterial community structures already were seen on TTGE profiles and no additional analysis was needed. We suggest the use of P. scaber gut bacterial community structure as a measure of effects caused by both long- and short-term exposure to pollution.