Microbial Functional Capacity Research Articles

Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence

BackgroundBoreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing.ResultsFungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion.ConclusionsMicrobial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.

Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity.

The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.

Composition, function, and timing: exploring the early-life gut microbiota in piglets for probiotic interventions

BackgroundThe establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous effects. However, the optimal timeframe for introducing probiotics to achieve this outcome remains uncertain.ResultsIn the context of this investigation, we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time points. Simultaneously, we gathered vaginal and fecal samples from 23 sows. Employing 16S rRNA gene and metagenomic sequencing methodologies, we conducted a comprehensive analysis of the fluctuation patterns in microbial composition, functional capacity, interaction networks, and colonization resistance within the gut microbiota of piglets. As the piglets progressed in age, discernible modifications in intestinal microbial diversity, composition, and function were observed. A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal piglets. By D21, the microbial interaction network displayed a more concise and efficient configuration, accompanied by enhanced colonization resistance relative to the other two time points. Moreover, we identified three strains of Ruminococcus sp. at D10 as potential candidates for improving piglets' weight gain during the weaning phase.ConclusionsThe findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet development. This investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.

The microbiome of African penguins (Spheniscus demersus) under managed care resembles that of wild marine mammals and birds

Animals under managed care in zoos and aquariums are ideal surrogate study subjects for endangered species that are difficult to obtain in the wild. We compared the fecal and oral microbiomes of healthy, managed African penguins (Spheniscus demersus) to those of other domestic and wild vertebrate hosts to determine how host identity, diet, and environment shape the penguin microbiome. The African penguin oral microbiome was more similar to that of piscivorous marine mammals, suggesting that diet and a marine environment together play a strong role in shaping the oral microbiome. Conversely, the penguin cloaca/fecal microbiome was more similar to that of other birds, suggesting that host phylogeny plays a significant role in shaping the gut microbiome. Although the penguins were born under managed care, they had a gut microbiome more similar to that of wild bird species compared to domesticated (factory-farmed) birds, suggesting that the managed care environment and diet resemble those experienced by wild birds. Finally, the microbiome composition at external body sites was broadly similar to that of the habitat, suggesting sharing of microbes between animals and their environment. Future studies should link these results to microbial functional capacity and host health, which will help inform conservation efforts.

Crop rotation-driven changes in rhizosphere metabolite profiles regulate soil microbial diversity and functional capacity

Plants are increasingly revealed to have the ability to shape microbiome composition and function by triggering rhizosphere metabolites. Rotation, a model of crop diversification, promotes crop production by influencing rhizosphere microbiome. However, the rhizosphere metabolites of different rice rotations are rarely reported and, in particular, the regulation of key metabolites on rhizosphere microbiome is unclear. To address this gap, we collected the bulk and rhizosphere soils of four crop rotations (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) to assess rhizosphere metabolites, soil bacterial and fungal diversity, as well as functional microbial populations from a long-term (more than 20 years) field experiment. Compared with the rice-rice system, rhizosphere metabolites, such as deazaflavin, 10-Deacetylbaccatin III, and paclobutrazol, significantly increased in the rice rotation systems with tobacco and oilseed rape. Metabolite components (e.g., azelaic acid, soyasapogenol B, and canrenone) and microbial taxa (Xanthobacteraceae, Bradyrhizobium, and Mortierella) were the keystones regulating the co-occurring correlations of rhizosphere metabolites and soil microorganisms. Compared with the rice-rice, the bulk and rhizosphere soil of rice rotations with oilseed rape or tobacco showed higher abundance of the microbial populations related to C degradation and fixation, N fixation, nitrification, nitrate reduction, inorganic P (Pi) solubilization, and organic P (Po) mineralization. Metabolites, such as 7-chloro-norlichexanthone, daidzein, and soyasapogenol B, were the keystones regulating the co-occurrence relationships of rhizosphere metabolites and functional microbial populations. Rhizosphere metabolite composition was positively related to the populations associated with C fixation and degradation, nitrification, and P solubilization, and negatively related to those associated with methane metabolism, nitrate reduction, denitrification, and anammox (P ≤ 0.05). Soyasapogenol B, daidzei, and [1,1'-biphenyl]− 2,2'-dicarboxylic acid enriched in rotation systems were negatively correlated with dominant microbial taxa such as phylum Bacteroidetes and Chytridiomycota, and positively correlated with phylum Zoopagomycota and the populations associated with key soil functions such as C degradation, nitrate reduction, and P solubilization (P ≤ 0.05). These results demonstrated the importance of rhizosphere metabolites in regulating soil microbiome composition and functional capacity, which deepens understanding of rotations improving rice production via rhizosphere effect.

House ammonia exposure causes alterations in microbiota, transcriptome, and metabolome of rabbits.

Pollutant gas emissions in the current production system of the livestock industry have negative influences on environment as well as the health of farm staffs and animals. Although ammonia (NH3) is considered as the primary and harmful gas pollutant in the rabbit farm, less investigation has performed to determine the toxic effects of house ammonia exposure on rabbit in the commercial confined barn. In this study, we performed multi-omics analysis on rabbits exposed to high and low concentration of house ammonia under similar environmental conditions to unravel the alterations in nasal and colonic microbiota, pulmonary and colonic gene expression, and muscular metabolic profile. The results showed that house ammonia exposure notably affected microbial structure, composition, and functional capacity in both nasal and colon, which may impact on local immune responses and inflammatory processes. Transcriptome analysis indicated that genes related to cell death (MCL1, TMBIM6, HSPB1, and CD74) and immune response (CDC42, LAMTOR5, VAMP8, and CTSB) were differentially expressed in the lung, and colonic genes associated with redox state (CAT, SELENBP1, GLUD1, and ALDH1A1) were significantly up-regulated. Several key differentially abundant metabolites such as L-glutamic acid, L-glutamine, L-ornithine, oxoglutaric acid, and isocitric acid were identified in muscle metabolome, which could denote house ammonia exposure perturbed amino acids, nucleotides, and energy metabolism. In addition, the widespread and strong inter-system interplay were uncovered in the integrative correlation network, and central features were confirmed by in vitro experiments. Our findings disclose the comprehensive evidence for the deleterious effects of house ammonia exposure on rabbit and provide valuable information for understanding the underlying impairment mechanisms.

The animal's microbiome and cancer: a translational perspective.

Cancer is a substantial global health problem both in humans and animals with a consistent increase in mortality and incidence rate. The commensal microbiota has been involved in the regulation of several physiological and pathological processes, both within the gastrointestinal system and at distant tissue locations. Cancer isn't an exception, and different aspects of the microbiome have been described to have anti- or pro-tumour effects. Using new techniques, for example high-throughput DNA sequencing, microbial populations of the human body have been largely described and, in the last years, studies more focused on companions' animals have emerged. In general, the recent investigations of fecal microbial phylogeny and functional capacity of the canine and feline gut have shown similarities with human gut. In this translational study we will review and summarize the relation between the microbiota and cancer, in humans and companion animals, and compare their resemblance in the type of neoplasms already studied in veterinary medicine: multicentric and intestinal lymphoma, colorectal tumours, nasal neoplasia and mast cell tumours. In the context of One Health, microbiota and microbiome integrative studies may contribute to the understanding of the tumourigenesis process, besides offering an opportunity to develop new diagnostics and therapeutic biomarkers both for veterinary and human oncology.

Microbial activity and habitat heterogeneity in surface soil in a high-mountain grassland landscape (Central Apennines, Italy)

A spatially intensive sampling of surface soil layers (81 stratified-randomized sampling points across a 14 km2 study area) was performed in a high-mountain grassland landscape (Central Apennines, Italy) in July 2017, in order to describe the heterogeneity of microbial habitats and measure their microbial enzymatic activity. Three different microbial habitat types were identified via Hierarchical Cluster Analysis on the basis of 14 (measured or remote-sensed) environmental variables (including chemical and physical soil properties, topographic and geomorphological features and vegetation cover): (i) sub-acidic, at high elevation, with high vegetation cover (of mostly acidophytic/mesophytic species) and high silt content, and the lowest clay content; (ii) sub-acidic, at low elevation, with a high vegetation cover and a very low stone cover, with the highest sand and the lowest silt content, and the highest available phosphorus; (iii) very shallow soil, mainly stone-covered, at high elevation, with the highest pH values, on steep slopes, with the highest content of organic matter and the highest water holding capacity. The third habitat showed the highest enzymatic activity (b-glucosidase, β-cellobiohydrolase and leucine-arylamidase) involved in C and N cycling, while the more acidic and deeper soils, typical of sinkhole or slope areas, favoured the acid phosphomonoesterase activity involved in P cycle thanks to the establishment of the rhizospheric activity of the herbaceous plant species. Moreover, we analysed the relative importance of environmental variables on the total enzyme activities via Boosted Regression Trees (BRT): the results highlighted - for the first time as far as we know - the importance of topographic factors such as slope inclination in predicting the microbial functional capacity in a mountain grassland ecosystem. We conclude that the different enzymatic activity patterns found in the three habitats suggest diverse microbial functions with respect to nutrient cycling, within a small landscape and a relatively homogeneous land-cover.

IL-22 alters gut microbiota composition and function to increase aryl hydrocarbon receptor activity in mice and humans

BackgroundIL-22 is induced by aryl hydrocarbon receptor (AhR) signaling and plays a critical role in gastrointestinal barrier function through effects on antimicrobial protein production, mucus secretion, and epithelial cell differentiation and proliferation, giving it the potential to modulate the microbiome through these direct and indirect effects. Furthermore, the microbiome can in turn influence IL-22 production through the synthesis of L-tryptophan (L-Trp)-derived AhR ligands, creating the prospect of a host-microbiome feedback loop. We evaluated the impact IL-22 may have on the gut microbiome and its ability to activate host AhR signaling by observing changes in gut microbiome composition, function, and AhR ligand production following exogenous IL-22 treatment in both mice and humans.ResultsMicrobiome alterations were observed across the gastrointestinal tract of IL-22-treated mice, accompanied by an increased microbial functional capacity for L-Trp metabolism. Bacterially derived indole derivatives were increased in stool from IL-22-treated mice and correlated with increased fecal AhR activity. In humans, reduced fecal concentrations of indole derivatives in ulcerative colitis (UC) patients compared to healthy volunteers were accompanied by a trend towards reduced fecal AhR activity. Following exogenous IL-22 treatment in UC patients, both fecal AhR activity and concentrations of indole derivatives increased over time compared to placebo-treated UC patients.ConclusionsOverall, our findings indicate IL-22 shapes gut microbiome composition and function, which leads to increased AhR signaling and suggests exogenous IL-22 modulation of the microbiome may have functional significance in a disease setting.Cw21cUiGabCHLYfc9EL5iqVideo

Week-Old Chicks with High Bacteroides Abundance Have Increased Short-Chain Fatty Acids and Reduced Markers of Gut Inflammation.

As important commensals in the chicken intestine, Bacteroides are essential complex carbohydrate degraders, and short-chain fatty acid (SCFA) producers that are highly adapted to the distal gut. Previous studies have shown large variation in Bacteroides abundance in young chickens. However, limited information is available regarding how this variation affects the gut microbiome and host immunity. To investigate how elevated or depleted Bacteroides levels affect gut microbial functional capacity and impact host response, we sampled 7-day-old broiler chickens from 14 commercial production flocks. Week-old broiler chickens were screened and birds with low Bacteroides (LB) and high Bacteroides (HB) abundance were identified via 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) assays. Cecal microbial functionality and SCFA concentration of chickens with distinct cecal Bacteroides abundance were profiled by shotgun metagenomic sequencing and gas chromatography, respectively. The intestinal immune responses of LB and HB chickens were assessed via reverse transcription qPCR. Results showed that the gut microbiota of the LB group had increased abundance of lactic acid bacteria pyruvate fermentation pathway, whereas complex polysaccharide degradation and SCFA production pathways were enriched in the HB group (P < 0.05), which was supported by increased SCFA concentrations in the ceca of HB chickens (P < 0.05). HB chickens also showed decreased expression of interleukin-1β and increased expression of interleukin-10 and tight-junction protein claudin-1 (P < 0.05). Overall, the results indicated that elevated Bacteroides may benefit the 7-day broiler gut and that further work should be done to confirm the causal role of Bacteroides in the observed positive outcomes. IMPORTANCE To date, limited information is available comparing distinct Bacteroides compositions in the chicken gut microbial communities, particularly in the context of microbial functional capacities and host responses. This study showed that possessing a microbiome with elevated Bacteroides in early life may confer beneficial effects to the chicken host, particularly in improving SCFA production and gut health. This study is among the first metagenomic studies focusing on the early life chicken gut microbiota structure, microbial functionality, and host immune responses. We believe that it will offer insights to future studies on broiler gut microbial population and their effects on host health.

The correlation between dysfunctional intestinal flora and pathology feature of patients with pulmonary tuberculosis.

Recent studies have provided insights into the important contribution of gut microbiota in the development of Pulmonary Tuberculosis (PTB). As a chronic consumptive infectious disease, PTB involves many pathological characteristics. At present, research on intestinal flora and clinical pathological Index of PTB is still rare. We performed a cross-sectional study in 63 healthy controls (HCs) and 69 patients with untreated active PTB to assess the differences in their microbiota in feces via 16S rRNA gene sequencing. Significant alteration of microbial taxonomic and functional capacity was observed in PTB as compared to the HCs. The results showed that the alpha diversity indexes of the PTB patients were lower than the HCs (P<0.05). Beta diversity showed differences between the two groups (P<0.05). At the genus level, the relative abundance of Bacteroides, Parabacteroides and Veillonella increased, while Faecalibacterium, Bifidobacterium, Agathobacter and CAG-352 decreased significantly in the PTB group, when compared with the HCs. The six combined genera, including Lactobacillus, Faecalibacterium, Roseburia, Dorea, Monnoglobus and [Eubacterium]_ventriosum_group might be a set of diagnostic biomarkers for PTB (AUC=0.90). Besides, the predicted bacterial functional pathway had a significant difference between the two groups (P<0.05), which was mainly related to the nutrient metabolism pathway. Significant alterations in the biochemical index were associated with changes in the relative abundance of specific bacteria, the short chain fatty acid (SCFA)-producing bacteria enriched in HCs had a positively correlated with most of the biochemical indexes. Our study indicated that the gut microbiota in PTB patients was significantly different from HCs as characterized by the composition and metabolic pathway, which related to the change of biochemical indexes in the PTB group. It was hypothesized that the abovementioned changes in the gut microbiota could exert an impact on the clinical characteristics of PTB through the regulation of the nutrient utilization pathway of the host by way of the gut-lung axis.

Tillage and pesticide seed treatments have distinct effects on soil microbial diversity and function

Conservation tillage practices can benefit soil health relative to conventional tillage; however, conservation tillage systems are often coupled with the use of pesticide seed treatments (PST; fungicides and insecticides, including neonicotinoids), which may undermine these benefits by disrupting microbial communities and processes. We examined the effects of tillage system (conventional moldboard plowing versus two conservation tillage practices: no tillage and strip tillage) and PST on microbial diversity and microbial function in a field experiment with a soybean–corn rotation. Enzyme activities and the microbial functional capacity to degrade a variety of substrates was intermediate in strip tillage compared with conventional and no tillage. Microbial community composition under strip tillage was similar to those under no tillage but distinct from conventional tillage, and community differences were associated with soil C/N and pH. However, tillage system had no effect on alpha diversity. Communities under strip tillage and no tillage had different substrate preferences to those under conventional tillage, which could be explained by the major C sources under each management practice. Pesticide seed treatment affected microbial substrate preference and altered the relative abundance of various fungal taxa, indicating a direct (i.e., toxic) effect. Despite this, PST had no effect on enzyme activities or alpha diversity of the microbial community. There were limited interactions between tillage and PST on microbial properties. Our results support that microbial communities are valuable indicators of soil health and show that strip tillage maintains soil microbial health better than conventional tillage but not as well as no tillage, and that PST may negatively affect soil microbial health.

Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands.

In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.

Enhanced susceptibility to oiling may limit denitrification recovery in marshes subjected to woody encroachment

Coastal salt marshes provide valuable ecosystem services but are subjected to multiple concomitant stressors that may impact their ability to provide those services. Global climate change has led to the poleward expansion of mangroves into salt marshes on each continent where mangroves and marshes co-occur. In the northern Gulf of Mexico, warming winter temperatures have resulted in the expansion of Avicennia germinans (black mangrove) into forb-dominated salt marshes, resulting in a shift in ecosystem structure that can impact the ecosystem services marshes provide, including biogeochemical processes such as nitrogen removal. There have been limited studies addressing how mangrove expansion impacts nitrogen removal rates in salt marshes, but it is possible that mangroves enhance microbial nitrogen removal capacity through more efficient oxygen translocation to sediments. However, mangroves are more sensitive to oiling (such as occurred during the 2010 Deepwater Horizon spill) than marsh plants, such as Spartina alterniflora, which have a higher turnover. Thus, even if they enhance nitrogen removal, if they cannot withstand disturbances such as oiling, there still may be a loss of function associated with woody encroachment. We conducted a field study to assess the impact of woody encroachment in mediating biogeochemical recovery 7 to 8 years after the Deepwater Horizon oil spill. We collected sediments from S. alterniflora- and A. germinans-dominated plots in the Chandeleur Islands (LA, United States), a chain of barrier islands in the northern Gulf of Mexico subjected to a range of oiling following the spill. We compared nitrate reduction rates (denitrification and dissimilatory nitrate reduction to ammonium), microbial community composition, and denitrifier marker gene abundance at sites subjected to light and moderate oiling using a combination of isotope pairing on sediment slurries, 16S sequencing, and qPCR. We predicted that overall, denitrification rates and microbial functional capacity would be enhanced in mangrove-dominated sediments. We also predicted that these enhancements would be diminished at the more intensely oiled site due to the higher susceptibility of A. germinans to oiling. Denitrification potential rates were higher in mangrove sediments at the lightly oiled site, whereas dissimilatory nitrate reduction to ammonium potential rates were higher in marsh sediments. Indicator analysis of 16S rRNA data selected putative sulfur cycling taxa as indicators of marsh sediments, suggesting that changes in oxygen availability associated with encroachment may be driving the differences in process rates. There was no difference in process rates between plant types at the moderately oiled site, where heavily weathered oil residue was still present. Sediment nutrient stocks were lower in moderately oiled mangrove plots than in lightly oiled mangrove plots, suggesting that sediment fertility recovery following the spill may have been slower in the mangroves, contributing to a change in ecosystem function. This study shows that woody encroachment has the potential to impact both the biogeochemical services that marshes provide and their response to and recovery from disturbances.

Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial

Aims/hypothesisThe use of oral glucose-lowering drugs, particularly those designed to target the gut ecosystem, is often observed in association with altered gut microbial composition or functional capacity in individuals with type 2 diabetes. The gut microbiota, in turn, plays crucial roles in the modulation of drug efficacy. We aimed to assess the impacts of acarbose and vildagliptin on human gut microbiota and the relationships between pre-treatment gut microbiota and therapeutic responses.MethodsThis was a randomised, open-labelled, two-arm trial in treatment-naive type 2 diabetes patients conducted in Beijing between December 2016 and December 2017. One hundred participants with overweight/obesity and newly diagnosed type 2 diabetes were recruited from the Pinggu Hospital and randomly assigned to the acarbose (n=50) or vildagliptin (n=50) group using sealed envelopes. The treatment period was 6 months. Blood, faecal samples and visceral fat data from computed tomography images were collected before and after treatments to measure therapeutic outcomes and gut microbiota. Metagenomic datasets from a previous type 2 diabetes cohort receiving acarbose or glipizide for 3 months were downloaded and processed. Statistical analyses were applied to identify the treatment-related changes in clinical variables, gut microbiota and associations.ResultsNinety-two participants were analysed. After 6 months of acarbose (n=44) or vildagliptin (n=48) monotherapy, both groups achieved significant reductions in HbA1c (from 60 to 46 mmol/mol [from 7.65% to 6.40%] in the acarbose group and from 59 to 44 mmol/mol [from 7.55% to 6.20%] in the vildagliptin group) and visceral fat areas (all adjusted p values for pre–post comparisons <0.05). Both arms showed drug-specific and shared changes in relative abundances of multiple gut microbial species and pathways, especially the common reductions in Bacteroidetes species. Three months and 6 months of acarbose-induced changes in microbial composition were highly similar in type 2 diabetes patients from the two independent studies. Vildagliptin treatment significantly enhanced fasting active glucagon-like peptide-1 (GLP-1) levels. Baseline gut microbiota, rather than baseline GLP-1 levels, were strongly associated with GLP-1 response to vildagliptin, and to a lesser extent with GLP-1 response to acarbose.Conclusions/interpretationThis study reveals common microbial responses in type 2 diabetes patients treated with two glucose-lowering drugs targeting the gut differently and acceptable performance of baseline gut microbiota in classifying individuals with different GLP-1 responses to vildagliptin. Our findings highlight bidirectional interactions between gut microbiota and glucose-lowering drugs.Trial registrationClinicalTrials.gov NCT02999841FundingNational Key Research and Development Project: 2016YFC1304901.Graphical abstract

Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers

Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18–30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.

Metagenomic analysis reveals microbial community and functional capacity in Kombucha

Kombucha is a traditional beverage obtained from fermented sugar-tea by a community of bacteria and yeasts. Understanding the microbial composition and their functions in Kombucha fermentation is of significance, but most of the studies have relied on the culture-dependent method. In this study, a metagenomic analysis was conducted to obtain a more comprehensive insight into Kombucha fermentation. Results showed that the bacteria of Kombucha were dominated by Komagataeibacter (36.24 to 63.35%), Gluconacetobacter (10.39 to 26.21%), Gluconobacter (6.62 to 27.10%), Acetobacter (0.3 to 6.64%), and the fungus Kluyveromyces (0.63 to 36.98%) was also identified. Taxonomic composition and abundance of the microbial community were distinct with each Kombucha sample. The carbohydrate active enzyme functions of the communities primarily comprised glycosyltransferase (GT) families (40.6%), glycoside hydrolase (GH) families (32.0%), and carbohydrate-binding module (CBM) fam-ilies (12.9%). Moreover, functional genes and their KEGG pathways were predicted, which demonstrated that the functional genes present in the bacterial community were enriched in pathways for neurodegenerative disease, amino acid metabolism, metabolism of cofactors and vitamins, carbohydrate metabolism, folding, sorting and degradation, and translation. The results of this study would provide a better understanding of the microbiota and metabolites as well as health-promoting potential of Kombucha, and may facilitate the optimization of the process to produce Kombucha products with desirable qualities.

Microbial Community Structure Is Most Strongly Associated With Geographical Distance and pH in Salt Lake Sediments.

Salt lakes are globally significant microbial habitats, hosting substantial novel microbial diversity and functional capacity. Extremes of salinity and pH both pose major challenges for survival of microbial life in terrestrial and aquatic environments, and are frequently cited as primary influences on microbial diversity across a wide variety of environments. However, few studies have attempted to identify spatial and geochemical contributions to microbial community composition, functional capacity, and environmental tolerances in salt lakes, limiting exploration of novel halophilic and halotolerant microbial species and their potential biotechnological applications. Here, we collected sediment samples from 16 salt lakes at pH values that ranged from pH 4 to 9, distributed across 48,000 km2 of the Archaean Yilgarn Craton in southwestern Australia to identify associations between environmental factors and microbial community composition, and used a high throughput culturing approach to identify the limits of salt and pH tolerance during iron and sulfur oxidation in these microbial communities. Geographical distance between lakes was the primary contributor to variation in microbial community composition, with pH identified as the most important geochemical contributor to variation in microbial community composition. Microbial community composition split into two clear groups by pH: Bacillota dominated microbial communities in acidic saline lakes, whereas Euryarchaeota dominated microbial communities in alkaline saline lakes. Iron oxidation was observed at salinities up to 160 g L–1 NaCl at pH values as low as pH 1.5, and sulfur oxidation was observed at salinities up to 160 g L–1 NaCl between pH values 2–10, more than doubling previously observed tolerances to NaCl salinity amongst cultivable iron and sulfur oxidizers at these extreme pH values. OTU level diversity in the salt lake microbial communities emerged as the major indicator of iron- and sulfur-oxidizing capacity and environmental tolerances to extremes of pH and salinity. Overall, when bioprospecting for novel microbial functional capacity and environmental tolerances, our study supports sampling from remote, previously unexplored, and maximally distant locations, and prioritizing for OTU level diversity rather than present geochemical conditions.

Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli

ABSTRACT Previous studies have shown high acquisition risks of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among international travelers visiting antimicrobial resistance (AMR) hotspots. Although antibiotic use and travelers’ diarrhea have shown to influence the ESBL-E acquisition risk, it remains largely unknown whether successful colonization of ESBL-E during travel is associated with the composition, functional capacity and resilience of the traveler’s microbiome. The microbiome of pre- and post-travel fecal samples from 190 international travelers visiting Africa or Asia was profiled using whole metagenome shotgun sequencing. A metagenomics species concept approach was used to determine the microbial composition, population diversity and functional capacity before travel and how it is altered longitudinally. Eleven travelers were positive for ESBL-E before travel and removed from the analysis. Neither the microbial richness (Chao1), diversity (effective Shannon) and community structure (Bray–Curtis dissimilarity) in pretravel samples nor the longitudinal change of these metrics during travel were predictive for ESBL-E acquisition. A zero-inflated two-step beta-regression model was used to determine how the longitudinal change in both prevalence and abundance of each taxon was related to ESBL acquisition. There were detected increases in both the prevalence and abundance of Citrobacter freundii and two members of the genus Bacteroides, in association with remaining uncolonized by ESBL-E. These results highlight the potential of these individual microbes as a microbial consortium to prevent the acquisition of ESBL-E. The ability to alter a person’s colonization resistance to a bacterium could be key to intervention strategies that aim to minimize the spread of MDR bacteria.

Xanthohumol Requires the Intestinal Microbiota to Improve Glucose Metabolism in Diet-Induced Obese Mice.

The polyphenol xanthohumol (XN) improves dysfunctional glucose and lipid metabolism in diet-induced obesity animal models. Because XN changes intestinal microbiota composition, the study hypothesizes that XN requires the microbiota to mediate its benefits. To test the hypothesis, the study feeds conventional and germ-free male Swiss Webster mice either a low-fat diet (LFD, 10% fat derived calories), a high-fat diet (HFD, 60% fat derived calories), or a high-fat diet supplemented with XN at 60mg kg-1 body weight per day (HXN) for 10 weeks, and measure parameters of glucose and lipid metabolism. In conventional mice, the study discovers XN supplementation decreases plasma insulin concentrations and improves Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). In germ-free mice, XN supplementation fails to improve these outcomes. Fecal sample 16S rRNA gene sequencing analysis suggests XN supplementation changes microbial composition and dramatically alters the predicted functional capacity of the intestinal microbiota. Furthermore, the intestinal microbiota metabolizes XN into bioactive compounds, including dihydroxanthohumol (DXN), an anti-obesogenic compound with improved bioavailability. XN requires the intestinal microbiota to mediate its benefits, whichinvolves complex diet-host-microbiota interactions with changes in both microbial composition and functional capacity. The study results warrant future metagenomic studies which will provide insight into complex microbe-microbe interactionsand diet-host-microbiota interactions.