The microbiome has emerged as a new player on behavior, physiology and stress because of its significant effects on the brain-gut axis. The aim of this study was to increase our understanding of ...brain-gut function in dairy cows. We investigated the effects of a heat-stress (HS) environment and individual differences of heat sensitivity (IH) on bovine physiological characteristics and microbial composition. Results indicate that both HS and IH increased rectal temperature (RT) (P < 0.05). An HS environment increased plasma, as well as milk cortisol and cytokines in plasma; however, it decreased plasma, and milk oxytocin, triiodothyronine, and thyroxine (P < 0.05) levels. Exposure to an HS environment reduced the diversity of the fecal microbial population, and resulted in a higher expression of diseases, the environmental adaptation pathway, and the immune related pathway, whereas it lowered the expression of metabolic pathways (P < 0.05). High heat sensitive cows have upregulated metabolisms, environmental adaptation and cellular process pathways, and a downregulated neurodegenerative disease pathway (P < 0.05). Thus, we conclude that exposure to an HS environment modulates physiological characteristics, which may interplay with microbial activity, and in turn, alter the circulation levels of cytokines, implicating the role of the brain-gut axis in dairy cows. The HS environment affected physiological characteristics, cytokine levels, and microbial composition, but IH influenced RT and fecal microbial functions.
•Impacts of different operational parameters on function microbes were evaluated.•Function microbiomes included the distinct and overlapping components.•The set of minimal “core microbiome” is ...detectable (ca. 40%).•Organic loading rate shaped finer microbial networks than hydraulic retention time.•Firmicutes is the most connected node with biogas production.
Understanding of how anaerobic digestion (AD)-related microbiomes are constructed by operational parameters or their interactions within the biochemical process is limited. Using high-throughput sequencing and molecular ecological network analysis, this study shows the succession of AD-related microbiome hosting diverse members of the phylum Actinobacteria, Bacteroidetes, Euryarchaeota, and Firmicutes, which were affected by organic loading rate (OLR) and hydraulic retention time (HRT). OLR formed finer microbial network modules than HRT (12 vs. 6), suggesting the further subdivision of functional components. Biomarkers were also identified in OLR or HRT groups (e.g. the family Actinomycetaceae, Methanosaetaceae and Aminiphilaceae). The most pair-wise link between Firmicutes and biogas production indicates the keystone members based on network features can be considered as markers in the regulation of AD. A set of 40% species (“core microbiome”) were similar across different digesters. Such noteworthy overlap of microbiomes indicates they are generalists in maintaining the ecological stability of digesters.
Microbiome community typing analyses have recently identified the Bacteroides2 (Bact2) enterotype, an intestinal microbiota configuration that is associated with systemic inflammation and has a high ...prevalence in loose stools in humans
. Bact2 is characterized by a high proportion of Bacteroides, a low proportion of Faecalibacterium and low microbial cell densities
, and its prevalence varies from 13% in a general population cohort to as high as 78% in patients with inflammatory bowel disease
. Reported changes in stool consistency
and inflammation status
during the progression towards obesity and metabolic comorbidities led us to propose that these developments might similarly correlate with an increased prevalence of the potentially dysbiotic Bact2 enterotype. Here, by exploring obesity-associated microbiota alterations in the quantitative faecal metagenomes of the cross-sectional MetaCardis Body Mass Index Spectrum cohort (n = 888), we identify statin therapy as a key covariate of microbiome diversification. By focusing on a subcohort of participants that are not medicated with statins, we find that the prevalence of Bact2 correlates with body mass index, increasing from 3.90% in lean or overweight participants to 17.73% in obese participants. Systemic inflammation levels in Bact2-enterotyped individuals are higher than predicted on the basis of their obesity status, indicative of Bact2 as a dysbiotic microbiome constellation. We also observe that obesity-associated microbiota dysbiosis is negatively associated with statin treatment, resulting in a lower Bact2 prevalence of 5.88% in statin-medicated obese participants. This finding is validated in both the accompanying MetaCardis cardiovascular disease dataset (n = 282) and the independent Flemish Gut Flora Project population cohort (n = 2,345). The potential benefits of statins in this context will require further evaluation in a prospective clinical trial to ascertain whether the effect is reproducible in a randomized population and before considering their application as microbiota-modulating therapeutics.
Oscillospira is a common yet rarely cultivated gut bacterial genus. Recently human gut microbiota studies have demonstrated its underlying significance for host health. However, little is known about ...Oscillospira-related host information and the links between Oscillospira and other members of the gut microbial community. To study the ecology of Oscillospira and gain insights into Oscillospira-related host physiological conditions, we analyzed data from the Guangdong Gut Microbiome Project, one of the largest gut microbiota database currently. Data of 6376 participants were analyzed. We studied the prevalence and relative abundance of Oscillospira as well as the profiles of associated microbial communities. We found that Oscillospira is closely related to human health because its abundance was positively correlated with microbial diversity, high density lipoprotein, and sleep time, and was inversely correlated with diastolic blood pressure, systolic blood pressure, fasting blood glucose, triglyceride, uric acid and Bristol stool type. Moreover, random forest analysis with five-fold cross validation showed Oscillospira could be a predictor of low BMI and constipation in the subset. Overall, in this study, we provide a basic understanding of Oscillospira-related microbiota profile and physiological parameters of the host. Our results indicate Oscillospira may play a role in aggravating constipation.
Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand ...the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.
The intestinal mucosa serves both as a conduit for the uptake of food-derived nutrients and microbiome-derived metabolites, and as a barrier that prevents tissue invasion by microorganisms and ...tempers inflammatory responses to the myriad contents of the lumen. How the intestine coordinates physiological and immune responses to food consumption to optimize nutrient uptake while maintaining barrier functions remains unclear. Here we show in mice how a gut neuronal signal triggered by food intake is integrated with intestinal antimicrobial and metabolic responses that are controlled by type-3 innate lymphoid cells (ILC3)
. Food consumption rapidly activates a population of enteric neurons that express vasoactive intestinal peptide (VIP)
. Projections of VIP-producing neurons (VIPergic neurons) in the lamina propria are in close proximity to clusters of ILC3 that selectively express VIP receptor type 2 (VIPR2; also known as VPAC2). Production of interleukin (IL)-22 by ILC3, which is upregulated by the presence of commensal microorganisms such as segmented filamentous bacteria
, is inhibited upon engagement of VIPR2. As a consequence, levels of antimicrobial peptide derived from epithelial cells are reduced but the expression of lipid-binding proteins and transporters is increased
. During food consumption, the activation of VIPergic neurons thus enhances the growth of segmented filamentous bacteria associated with the epithelium, and increases lipid absorption. Our results reveal a feeding- and circadian-regulated dynamic neuroimmune circuit in the intestine that promotes a trade-off between innate immune protection mediated by IL-22 and the efficiency of nutrient absorption. Modulation of this pathway may therefore be effective for enhancing resistance to enteropathogens
and for the treatment of metabolic diseases.
Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and ...agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.
Bacteria and fungi form complex communities (microbiomes) in above- and below-ground organs of plants, contributing to hosts' growth and survival in various ways. Recent studies have suggested that ...host plant genotypes control, at least partly, plant-associated microbiome compositions. However, we still have limited knowledge of how microbiome structures are determined in/on grafted crop plants, whose above-ground (scion) and below-ground (rootstock) genotypes are different with each other. By using eight varieties of grafted tomato plants, we examined how rootstock genotypes could determine the assembly of leaf endophytic microbes in field conditions. An Illumina sequencing analysis showed that both bacterial and fungal community structures did not significantly differ among tomato plants with different rootstock genotypes: rather, sampling positions in the farmland contributed to microbiome variation in a major way. Nonetheless, a further analysis targeting respective microbial taxa suggested that some bacteria and fungi could be preferentially associated with particular rootstock treatments. Specifically, a bacterium in the genus Deinococcus was found disproportionately from ungrafted tomato individuals. In addition, yeasts in the genus Hannaella occurred frequently on the tomato individuals whose rootstock genotype was "Ganbarune". Overall, this study suggests to what extent leaf microbiome structures can be affected/unaffected by rootstock genotypes in grafted crop plants.
The herbicide “fomesafen” causes phytotoxicity to the rotational wheat crop and may reduce its yield. Considering that biochar may improve remediation and biophysical conditions of the contaminated ...soil environments to benefit plant growth. Here, we investigated the impacts of three levels of the wheat straw-derived biochar (1%, 2%, and 4% (w/w)) on growth, physiological properties, and rhizosphere microbial communities of the wheat (Triticum aestivum) seedlings under the fomesafen stress using high-throughput sequencing. The results showed that biochar amended into soil significantly reduced the uptake of wheat to fomesafen and thereby eliminate its toxicity to wheat seedlings. Moreover, biochar increased the abundance and diversity of plant beneficial bacterial and fungal taxa in the rhizosphere of wheat seedlings. Compared with the three addition amounts, amendment with 2% of biochar has the best effects to reduce the toxicity of fomesafen on wheat seedlings and maintain the balance of soil microbial community structure in soil contaminated with fomesafen (1.0 mg kg−1). Overall, our results suggest that the level of biochar application influences the structure and diversity of soil microbiome (and mycobiome) and plant performance under abiotic stress conditions.
Display omitted
•Biochar reduces fomesafen toxicity and improves wheat plant performance.•Biochar reduces the uptake of fomesafen by wheat roots.•Biochar increases soil microbiome and mycobiome diversity.•Biochar promotes beneficial root-microbe interactions under abiotic stress conditions.
In addition to its value in meat production, the pig is an interesting animal model for human digestive tract studies due to its physiological similarities. The aim of this study was to describe the ...microbiome composition, distribution and interaction along the Iberian pig intestinal tract and its role in whole-body energy homeostasis. The V3-V4 region of the 16S rRNA gene was amplified and sequenced from the microbiomes of five gut sections (duodenum, jejunum, ileum, and proximal and distal colon) in thirteen castrated male pigs. A total of 1,669 operational taxonomic units distributed in 179 genera were found among all samples. The two most abundant genera in the small intestine were Lactobacillus and Clostridium, while Prevotella was predominant in the colon. The colon samples were more similar among the pigs and richer in species than the small intestine samples were. In the small intestine, the metagenome prediction pointed to rapid internalization and conversion of the available simple carbohydrates for microbial proliferation and maintenance. In the colon, a competition among anaerobic bacteria for plant polysaccharide degradation to produce short chain fatty acids was found. This study confirms that the energy pathways of the gut microbiome differ along its sections and provides a description of the correlations between genera.
PDF
