Bacterial Relative Abundance Research Articles

A High Amylose Wheat Diet Improves Gastrointestinal Health Parameters and Gut Microbiota in Male and Female Mice.

High amylose wheat (HAW) contains more resistant starch than standard amylose wheat (SAW) and may have beneficial effects on gastrointestinal health. However, it is currently unclear whether these effects differ according to the level of HAW included in the diet or between males and females. Male and female C57BL/6 mice (n = 8/group/sex) were fed SAW65 (65% SAW; control), HAW35 (35% HAW), HAW50 (50% HAW) or HAW65 (65% HAW) diet for eight weeks. Female but not male, mice consuming any amount of HAW exhibited accelerated gastric emptying compared to SAW65 group. In both sexes, relative colon weights were higher in the HAW65 group compared to SAW65 group and in females, relative weights of the small intestine and cecum were also higher in the HAW65 group. In females only, colonic expression of Pyy and Ocln mRNAs were higher in the HAW65 group compared to HAW35 and HAW50 groups. In both sexes, mice consuming higher amounts of HAW (HAW50 or HAW65) had increased fecal bacterial load and relative abundance of Bacteroidetes phylum and reduced relative abundance of Firmicutes compared to SAW65 group. These data are consistent with a beneficial impact of HAW on gastrointestinal health and indicate dose-dependent and sex-specific effects of HAW consumption.

Endophytic Bacterial Communities in Apple Leaves Are Minimally Impacted by Streptomycin Use for Fire Blight Management

In apple fruit, streptomycin is routinely used to manage fire blight, a devastating disease that greatly affects commercial apple production. Applications of streptomycin may affect the endophytic bacterial communities, which are increasingly recognized for their valuable roles in plant hosts. Altering these communities may have implications for plant health and selection for streptomycin resistance in off-target bacteria. In a previous study, we found rapid selection of streptomycin-resistant epiphytes following season-long streptomycin use, and now sought to investigate the season-long impact of streptomycin applications (one, three, or nine postbloom applications) on endophytic bacterial communities. Studies were conducted in two orchards, and both culture-dependent and independent methods were used to assess the bacterial endophytic community. Streptomycin programs were compared with untreated trees and two programs approved for organic production. Treatments minimally affected abundance of culturable endophytic bacteria as determined by culture-dependent methods. Similarly, there were no significant differences in relative bacterial abundance or community composition between treatments as determined by 16S ribosomal RNA high-throughput sequencing (culture independent). There were greater differences between orchards than between treatments, suggesting a stronger influence of locality. Communities were dominated by the families Pseudomonadaceae, Enterobacteriaceae, Desulfovibrionaceae, Bacillaceae, and Burkholderiaceae, which are commonly described in other investigations of microbial communities of apple orchards. In addition, we found a high abundance of Amoebophiliaceae, a family dominated by arthropod parasites. Our results provide evidence that season-long applications of streptomycin in apple orchards have minimal impact on endophytic bacterial communities, which is in contrast to some reports on epiphytic communities.

SARS-CoV-2 infection in nonhuman primates alters the composition and functional activity of the gut microbiota

ABSTRACT The current pandemic of coronavirus disease (COVID) 2019 constitutes a global public health issue. Regarding the emerging importance of the gut-lung axis in viral respiratory infections, analysis of the gut microbiota’s composition and functional activity during a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection might be instrumental in understanding and controling COVID 19. We used a nonhuman primate model (the macaque), that recapitulates mild COVID-19 symptoms, to analyze the effects of a SARS-CoV-2 infection on dynamic changes of the gut microbiota. 16S rRNA gene profiling and analysis of β diversity indicated significant changes in the composition of the gut microbiota with a peak at 10–13 days post-infection (dpi). Analysis of bacterial abundance correlation networks confirmed disruption of the bacterial community at 10–13 dpi. Some alterations in microbiota persisted after the resolution of the infection until day 26. Some changes in the relative bacterial taxon abundance associated with infectious parameters. Interestingly, the relative abundance of Acinetobacter (Proteobacteria) and some genera of the Ruminococcaceae family (Firmicutes) was positively correlated with the presence of SARS-CoV-2 in the upper respiratory tract. Targeted quantitative metabolomics indicated a drop in short-chain fatty acids (SCFAs) and changes in several bile acids and tryptophan metabolites in infected animals. The relative abundance of several taxa known to be SCFA producers (mostly from the Ruminococcaceae family) was negatively correlated with systemic inflammatory markers while the opposite correlation was seen with several members of the genus Streptococcus. Collectively, SARS-CoV-2 infection in a nonhuman primate is associated with changes in the gut microbiota’s composition and functional activity.

Alterations of circulating bacterial DNA in colorectal cancer and adenoma: A proof-of-concept study.

The gut microbiota is closely associated with colorectal neoplasia. While most metagenomics studies utilized fecal samples, circulating bacterial DNA in colorectal neoplasia patients remained unexplored. This proof-of-concept study aims to characterize alterations of circulating bacterial DNA in colorectal neoplasia patients. We performed WGS of plasma samples from 25 colorectal cancer (CRC) patients, 10 colorectal adenoma (CRA) patients and 22 healthy controls (HC). Bacterial relative abundance was measured by removing the host genome and mapping reads into bacterial genomes. By diversity analysis, we found plasma samples required less sample size to approach saturation than fecal samples, and species diversity in HC was slightly higher compared with CRC/CRA patients. The majority of circulating bacterial DNA came from bacterial genera which commonly associated with gastrointestine and oral tract. By differential analysis, a total of 127 significant species between CRC patients and HC were identified, on which basis 28 species with top predictive ability were selected and showed promise in preliminary discrimination between CRC/CRA and HC. In CRA patients, relative abundance of the selected 28 species more closely resembled those in CRC patients than HC. By comparing with fecal metagenomics studies, we found there was moderate positive correlation between fold changes of the overlapped fecal and circulating bacterial DNA. Finally, species correlation analysis revealed that CRC and HC displayed distinct patterns of species association. In conclusion, this study demonstrated alterations of circulating bacterial DNA in colorectal neoplasia patients, which had the potential to become non-invasive biomarkers for colorectal neoplasia screening and early diagnosis.

Microbial function and genital inflammation in young South African women at high risk of HIV infection

BackgroundFemale genital tract (FGT) inflammation is an important risk factor for HIV acquisition. The FGT microbiome is closely associated with inflammatory profile; however, the relative importance of microbial activities has not been established. Since proteins are key elements representing actual microbial functions, this study utilized metaproteomics to evaluate the relationship between FGT microbial function and inflammation in 113 young and adolescent South African women at high risk of HIV infection. Women were grouped as having low, medium, or high FGT inflammation by K-means clustering according to pro-inflammatory cytokine concentrations.ResultsA total of 3186 microbial and human proteins were identified in lateral vaginal wall swabs using liquid chromatography-tandem mass spectrometry, while 94 microbial taxa were included in the taxonomic analysis. Both metaproteomics and 16S rRNA gene sequencing analyses showed increased non-optimal bacteria and decreased lactobacilli in women with FGT inflammatory profiles. However, differences in the predicted relative abundance of most bacteria were observed between 16S rRNA gene sequencing and metaproteomics analyses. Bacterial protein functional annotations (gene ontology) predicted inflammatory cytokine profiles more accurately than bacterial relative abundance determined by 16S rRNA gene sequence analysis, as well as functional predictions based on 16S rRNA gene sequence data (p < 0.0001). The majority of microbial biological processes were underrepresented in women with high inflammation compared to those with low inflammation, including a Lactobacillus-associated signature of reduced cell wall organization and peptidoglycan biosynthesis. This signature remained associated with high FGT inflammation in a subset of 74 women 9 weeks later, was upheld after adjusting for Lactobacillus relative abundance, and was associated with in vitro inflammatory cytokine responses to Lactobacillus isolates from the same women. Reduced cell wall organization and peptidoglycan biosynthesis were also associated with high FGT inflammation in an independent sample of ten women.ConclusionsBoth the presence of specific microbial taxa in the FGT and their properties and activities are critical determinants of FGT inflammation. Our findings support those of previous studies suggesting that peptidoglycan is directly immunosuppressive, and identify a possible avenue for biotherapeutic development to reduce inflammation in the FGT. To facilitate further investigations of microbial activities, we have developed the FGT-DB application that is available at http://fgtdb.org/.DwvYvmP_Lqo1TfCUgVQTWuVideo

The Gut Microbiome in Polycystic Ovary Syndrome and Its Association with Metabolic Traits.

Despite the gut microbiome being widely studied in metabolic diseases, its role in polycystic ovary syndrome (PCOS) has been scarcely investigated. Compare the gut microbiome in late fertile age women with and without PCOS and investigate whether changes in the gut microbiome correlate with PCOS-related metabolic parameters. Prospective, case-control study using the Northern Finland Birth Cohort 1966. General community. A total of 102 PCOS women and 201 age- and body mass index (BMI)-matched non-PCOS control women. Clinical and biochemical characteristics of the participants were assessed at ages 31 and 46 and analyzed in the context of gut microbiome data at the age of 46. (s): None. Bacterial diversity, relative abundance, and correlations with PCOS-related metabolic measures. Bacterial diversity indices did not differ significantly between PCOS and controls (Shannon diversity P = .979, unweighted UniFrac P = .175). Four genera whose balance helps to differentiate between PCOS and non-PCOS were identified. In the whole cohort, the abundance of 2 genera from Clostridiales, Ruminococcaceae UCG-002, and Clostridiales Family XIII AD3011 group, were correlated with several PCOS-related markers. Prediabetic PCOS women had significantly lower alpha diversity (Shannon diversity P = .018) and markedly increased abundance of genus Dorea (false discovery rate = 0.03) compared with women with normal glucose tolerance. PCOS and non-PCOS women at late fertile age with similar BMI do not significantly differ in their gut microbial profiles. However, there are significant microbial changes in PCOS individuals depending on their metabolic health.

Oleanolic acid protection against experimental autoimmune myocarditis modulates the microbiota and the intestinal barrier integrity

Abstract Background Autoimmune myocarditis is a cause of dilated cardiomyopathy and heart failure. Recent studies have indicated that leaky gut may allow environmental factors to enter the body and trigger the initiation/development of autoimmune disease. Moreover, there is a growing literature supporting that, beside myocardial fibrosis, a leaky intestinal barrier and gut dysbiosis are pathogenic factors linked to heart failure. The natural triterpene oleanolic acid (OA) has been shown to beneficially influence the severity of the experimental autoimmune myocarditis (EAM), a preclinical model of human myocarditis, via anti-oxidant and immunomodulatory mechanisms. Herein, we investigate gastrointestinal (GI) disturbances and the gut microbiota composition associated with EAM as potential therapeutic target of OA. Methods and results BALB/c mice were α-myosin-inmunized to induce EAM and treated with OA (25 mg/kg/day, i.p). On day 21, heart fibrosis and parameters related to gut damage such as oxidative stress (O2- ions, lipid peroxidation), gut permeability (D-lactate; I-FABP), inflammation and mucins were determined in serum and/or colon. Fecal microbial profiles were identified by 16S rRNA gene sequencing analysis. Firstly, histological analysis of hearts showed presence of fibrosis (Sirius Red stain) in EAM mice, whereas these effects were not detectable in myocardium from healthy or OA-treated EAM mice. In addition, OA preserved the mucin-containing goblet cells along the colon (Alcian Blue/PAS stain). Consistently, serum levels of the epithelial gut damage markers, including D-lactate and iFABP were significantly reduced in OA treated-EAM mice. The beneficial OA effects also included a decrease in the pro-inflammatory mediators sPLA2-IIA and IL-1β and a protection from the oxidative stress response (DHE stain and TBARS) in serum and colonic tissue of EAM-mice. Furthermore, gut microbiota composition showed a lower bacterial diversity and different relative abundance of certain bacterial taxa in EAM-mice compared to control mice. The families of Muribaculaceae, Lachnospiraceae, and Ruminococcaceae were significantly affected in EAM mice, and only Muribaculaceae recovered levels similar to the healthy-control group, after treatment with OA. Conclusion Our data show that in addition to the heart, the intestinal barrier and gut microbiota are altered in myocarditis, and that OA treatment could ameliorate this profile. Our data contribute to the idea that gut dysbiosis and GI dysfunction influences myocarditis pathogenesis, and provides new findings regarding the beneficial activity of OA in EAM, suggesting that it may be an interesting candidate to be explored for the treatment of human patients. Funding Acknowledgement Type of funding source: Public grant(s) – National budget only. Main funding source(s): MINECO, ISCIII, CIBERCV-ISCIII

Gut microbiota ecology: Biodiversity estimated from hybrid neutral-niche model increases with health status and aging.

In this work we propose an index to estimate the gut microbiota biodiversity using a modeling approach with the aim of describing its relationship with health and aging. The gut microbiota, a complex ecosystem that links nutrition and metabolism, has a pervasive effect on all body organs and systems, undergoes profound changes with age and life-style, and substantially contributes to the pathogenesis of age-related diseases. For these reasons, the gut microbiota is a suitable candidate for assessing and quantifying healthy aging, i.e. the capability of individuals to reach an advanced age, avoiding or postponing major age-related diseases. The importance of the gut microbiota in health and aging has been proven to be related not only to its taxonomic composition, but also to its ecological properties, namely its biodiversity. Following an ecological approach, here we intended to characterize the relationship between the gut microbiota biodiversity and healthy aging through the development a parsimonious model of gut microbiota from which biodiversity can be estimated. We analysed publicly available metagenomic data relative to subjects of different ages, countries, nutritional habits and health status and we showed that a hybrid niche-neutral model well describes the observed patterns of bacterial relative abundance. Moreover, starting from such ecological modeling, we derived an estimate of the gut microbiota biodiversity that is consistent with classical indices, while having a higher statistical power. This allowed us to unveil an increase of the gut microbiota biodiversity during aging and to provide a good predictor of health status in old age, dependent on life-style and aging disorders.

The Acute Effect of Meal Timing on the Gut Microbiome and the Cardiometabolic Health of the Host: A Crossover Randomized Control Trial

Purpose: The interaction of diet with gut microbiome has been implicated in the onset of cardiovascular disease. The gut microbiome displays diurnal rhythms, which may be influenced by meal timing. Objective: This study aimed to investigate the effect of the timing of main meal consumption on the microbiome and cardiometabolic biomarkers of the host. Methods: Seventeen healthy adults randomly consumed an isocaloric diet for 7 days, twice, by alternating lunch with dinner meals, and with a 2-week washout in-between. Sixty percent of the participants’ daily energy requirements was consumed either as lunch or dinner, respectively. Meals were provided free to the participants. All fecal samples produced the last 3 days of each intervention were collected and analyzed for microbial profiling (16S rRNA gene amplicon sequencing), quantitative estimation of representative bacterial groups (qPCR) of the gut microbiome, and the output of short-chain fatty acids (SCFA) in feces. Fasted blood samples were analyzed for low-grade inflammatory biomarkers, blood lipids, insulin, and glucose levels. Cumulative energy loss in feces was measured over the collection period using bomb calorimetry. Results: Meal timing had no significant effects on fecal SCFA output, energy loss in feces, microbial community profiling, and bacterial species relative abundance. The absolute concentration of Escherichia coli was significantly higher after the large lunch intervention (p = 0.02). No effects on blood biomarkers of cardiometabolic health were observed. Conclusions: In a well-controlled study, main meal timing displayed minimal acute effects on the gut microbiome composition, its diet-related function, and blood biomarkers of cardiometabolic health.

Correlation of the abundance of bacteria catalyzing phosphorus and nitrogen turnover in biological soil crusts of temperate forests of Germany

Soil P pools are strongly driven by microbial activities, and vice versa, P pools shape bacterial communities and their functional potential. Biological soil crusts (biocrusts) represent a microbial hotspot for nutrient turnover. We compared biocrusts and bulk soil samples from different temperate beech (Fagus sylvatica L.) forests representing a gradient in soil texture, nutrient concentrations, and pH values at biocrust peak biomass. We measured the total and plant-available P and N concentrations and assessed the bacterial potential to mineralize (phoD, phnX), solubilize (gcd), and take up P (pstS and pitA) and mineralize (chiA, apr) and fix N (nifH) by quantifying the respective marker genes (qPCR). We found an increase of absolute and relative bacterial abundance involved in P turnover in biocrusts, but the strategy to acquire P differed between the regions as bacteria harboring the starvation-induced pstS gene were most abundant where labile P was lowest. In contrast, the region with lowest total P concentrations has a higher potential to utilize more stable phosphonates. N mineralization was strongly correlated to P turnover at regions with increased labile N and P concentrations. Interestingly, the potential to fix N was highest in the bulk soil where total P concentrations were highest. Even though the correlation of N and P turnover is strongest if their ratio is low, the acquisition strategy strongly depends on soil properties.

Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term

BackgroundRecent studies suggest that alterations in the vaginal microbiome allow for the assessment of the risk for spontaneous preterm birth (PTB), the leading cause of neonatal morbidity and mortality worldwide. However, the associations between the local immune response and the vaginal microbiome are still poorly understood. Herein, we characterize the vaginal host immune-microbiome interactions in women who ultimately underwent PTB and in those who delivered at term. MethodsVaginal fluid samples from 52 pregnant women (of whom 18 underwent PTB and 34 delivered at term) were collected between 10 and 32 weeks of gestation in a case-control study. Concentrations of 33 immune mediators were determined using sensitive and specific immunoassays. The previously published 16S rRNA gene sequence and bacterial phylotype data of these subjects were utilized in this study. Linear mixed effects models were utilized to test associations between vaginal immune mediator concentrations and bacterial phylotype relative abundances. Results1) In the overall study population, vaginal concentrations of CXCL10, CCL2, CCL3, SLP1 and VEGF negatively correlated with non-Lactobacillus, Community State Type IV (CST IV) members of the vaginal microbiome; 2) CXCL10, in particular, negatively correlated with 15 bacterial phylotypes, most of which are typical members of CST IV, such as Gardnerella vaginalis, Megasphaera spp., and Atopobium vaginae; 3) Gemella spp., also members of CST IV, negatively correlated with vaginal concentrations of VEGF, CCL2, CCL3, SLPI, and CXCL10; 4) when comparing PTB cases to term controls, five soluble immune mediators (CCL26, CCL22, CCL2, CXCL10, and IL-16), especially CCL26, were negatively correlated with five typical members of CST IV: Sneathia sanguinegens, Parvimonas micra, Veillonellaceae, BVAB2, and Gemella spp.; and 5) Sneathia sanguinegens had stronger negative associations with all five soluble immune mediators (CCL26, CCL22, CCL2, CXCL10, and IL-16) in PTB cases than in term controls. ConclusionsThe assessment of vaginal host immune-microbiome interactions revealed that specific soluble immune mediators, mainly CXCL10, negatively correlated with typical members of CST IV of the vaginal microbiome. Sneathia sanguinegens, in particular, had stronger negative associations with different immune mediators, including CXCL10 and CCL26, in women who ultimately underwent PTB compared to those who delivered at term. These findings provide insight into the vaginal host immune-microbiome interactions in normal and complicated pregnancies.

The improvement of pollutant removal efficiency in saturated vertical flow constructed wetlands by tubifex tubifex

Pilot-scale saturated vertical flow constructed wetlands (VF-CWs) were established to identify whether T. tubifex has the similar performance in saturated VF-CWs to that in surface flow CWs in improving pollutant removal efficiency (RE). The saturated VF-CWs with T. tubifex achieved REs of 67.3% total nitrogen (TN) and 39.8% chemical oxygen demand (COD), which were significantly higher than treatments without T. tubifex (42.2% TN and 31.4% COD). There existed significant interactions between macrophytes and T. tubifex. T. tubifex greatly improved the dissolved oxygen by increasing the connectivity between layers, and enhanced dehydrogenase activity and fluorescein diacetate. Adding T. tubifex improved the bacterial diversity and relative abundance of both N-cycle bacteria and fermentation bacteria in the biofilms. The improvements of ammonia oxidation and anammox were the main pathways for the increased nitrogen removal by T. tubifex. Therefore, T. tubifex is a useful tool for improving pollutant REs in saturated VF-CWs.

Fine sediment and flow velocity impact bacterial community and functional profile more than nutrient enrichment.

Freshwater ecosystems face many simultaneous pressures due to human activities. Consequently, there has been a rapid loss of freshwater biodiversity and an increase in biomonitoring programs. Our study assessed the potential of benthic stream bacterial communities as indicators of multiple-stressor impacts associated with urbanization and agricultural intensification. We conducted a fully crossed four-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21d of colonization, 21d of manipulations) and investigated the effects of nutrient enrichment, flow-velocity reduction and added fine sediment after 2 and 3weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S rRNA genes), as well as curated biological databases (METAGENassit, MetaCyc), to identify changes in bacterial relative abundances and predicted metabolic functional profile. Sediment addition and flow-velocity reduction were the most pervasive stressors. They both increased α-diversity and had strong taxon-specific effects on community composition and predicted functions. Sediment and flow velocity also interacted frequently, with 88% of all bacterial response variables showing two-way interactions and 33% showing three-way interactions including nutrient enrichment. Changes in relative abundances of common taxa were associated with shifts in dominant predicted functions, which can be extrapolated to underlaying stream-wide mechanisms such as carbon use and bacterial energy production pathways. Observed changes were largely stable over time and occurred after just 2weeks of exposure, demonstrating that bacterial communities can be well-suited for early detection of multiple stressors. Overall, added sediment and reduced flow velocity impacted both bacterial community structure and predicted function more than nutrient enrichment. In future research and stream management, a holistic approach to studying multiple-stressor impacts should include multiple trophic levels with their functional responses, to enhance our mechanistic understanding of complex stressor effects and promote establishment of more efficient biomonitoring programs.

Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance

ABSTRACT Aging is associated with cognitive decline and decreased concentrations of short-chain fatty acids (SCFAs) in the gut. SCFAs are significant in that they are protective to the gut and other organs. We tested the hypothesis that the aged gut microbiome alone is sufficient to decrease SCFAs in the host and produce cognitive decline. Fecal transplant gavages (FTGs) from aged (18–20 months) or young (2–3 months) male C57BL/6 mice into germ-free male C57BL/6 mice (N = 11 per group) were initiated at ~3 months of age. Fecal samples were collected and behavioral testing was performed over the study period. Bacterial community structures and relative abundances were measured in fecal samples by sequencing the bacterial 16S ribosomal RNA gene. Mice with aged and young microbiomes showed clear differences in bacterial β diversity at 30, 60, and 90 d (P = .001 for each) after FTGs. The fecal SCFAs, acetate, propionate, and butyrate (microbiome effect, P < .01 for each) were decreased in mice with an aged microbiome. Mice with an aged microbiome demonstrated depressive-like behavior, impaired short-term memory, and impaired spatial memory over the 3 months following the initial FTG as assessed by the tail suspension (P = .008), the novel object recognition (P < .001), and the Barnes Maze (P = .030) tests, respectively. We conclude that an aged microbiome alone is sufficient to decrease SCFAs in the host and to produce cognitive decline.

Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs

BackgroundDiet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-week feeding trial, 6 lambs from each dietary treatment (SBM vs. DDGS-based diets) were slaughtered for sample collection. The microbiota of the rumen solid, liquid, and epithelium fractions was examined using amplicon sequencing analysis of bacterial 16S rRNA gene, functional prediction, and qPCR.ResultsNo interaction of dietary protein source (PS) and REN were detected for virtually all the measurements made in this study. The DDGS substitution resulted in very limited influence on bacterial community structure. However, the metabolic pathways predicted from 16S rRNA gene sequences varied greatly between SBM- and DDGS-based diets. The populations of rumen total bacteria, fungi, sulfate-reducing bacteria (SRB), and methanogens were not influenced by DDGS substitution, but the population of protozoa was reduced. The bacterial communities in rumen solid (RS) and liquid (RL) were similar in taxonomic composition but were different in relative abundance of some taxa. In contrast, the bacterial composition and relative abundance of rumen epithelium (RE) were greatly distinct from those of the RS and the RL. In alignment with the bacterial relative abundance, the metabolic pathways predicted from 16S rRNA genes also varied greatly among the different REN. The populations of total bacteria, protozoa, and methanogens attached to the RE were smaller than those in the RS and RL, and the fungal population on the rumen epithelium was smaller than that in the RS but similar to that in the RL. On the contrary, the SRB population on the RE was greater than that in the RS and RL.ConclusionsSubstitution of SBM with DDGS had greater impact to the protozoa than to the other microbes, and the microbial community structure and functions at different REN are distinct and niche-adapted.

Faecal calprotectin and gut microbiota do not predict enteropathy in very preterm infants.

AimVery preterm birth is associated with a high risk of enteropathies. Diagnosis is challenging, especially in mild forms, leading to unnecessary periods of cessation of enteral feeding. This study aimed at establishing a prognosis score of enteropathy combining clinical parameters and faecal calprotectin concentration.MethodsThis prospective multicentric study included preterm neonates born at a gestational age of 33 weeks or less. Stools were collected weekly until hospital discharge, and daily in case of digestive events for calprotectin measurement (ELISA and immunochromatography) and microbiota analyses (16S rRNA gene sequencing).ResultsAmong the 121 neonates included, 21 experienced at least one episode of enteropathy, mainly mild forms. By ELISA testing, median faecal calprotectin was 88 (8‐798) µg/g faeces. No statistically significant association was found between the outset of enteropathy and maternal and neonatal characteristics, and calprotectin levels. The agreement between ELISA and immunochromatography assay was moderate (intra‐class correlation coefficient 0.58, 95%CI [0.47‐0.66]). Comparison of species diversity and relative bacterial abundance profiles between infants with or without enteropathy revealed no specific alterations associated with enteropathy.ConclusionThe study failed to propose a prognostic score of enteropathy, probably due the large inter‐ and intra‐individual variability of faecal calprotectin in very preterm neonates.

Composition, predicted functions, and co-occurrence networks of fungal and bacterial communities_ Links to soil organic carbon under long-term fertilization in a rice-wheat cropping system

Soil microbial community compositions and soil labile organic carbon (LOC) fractions change rapidly in response to fertilizers and crop rotation, but our understanding of the associations between specific microbial taxa and C fractions is still limited. The objective of this study was to compare the composition and function of soil bacterial and fungal communities in response to fertilization and crop rotation and their correlations with LOC fractions. Communities were analyzed by PCR-amplification of bacterial 16S rRNA gene and fungal ITS sequences from soil DNA. Functions were predicted by in-silico tools. A long-term experimental rice-wheat cropping system was studied, and the soil collected from plots treated with different fertilizers, including a control without fertilizer (CK), inorganic nitrogen, phosphorous, and potassium (NPK), manure (M), and NPKM, was analyzed. Fertilizations, non-crop types, significantly modified the soil bacterial community composition and suspected functions, while both fertilization and crop types significantly affected the fungal community composition. Compared with CK, NPKM treatment significantly increased the relative bacterial abundances of Candidatus Solibacter, Nitrosporia, Geobacter and Bryobacter, but decreased the relative fungal abundances of Paraphaeosphaeria sporulosa, Emericellopsis, Cladosporium tennuissimum, Curvularia lunata, Stachybotrys chlorolonate and Moleospora. All responding OTUs correlated significantly with soil LOC fractions, especially particulate organic C. The suspected functions suggest that organic amendment provided larger quantities of organic C, then promoting the growth of microorganism involved in C degradation, which in turn contributing to C sequestration. Our results indicate that fertilizers and crop rotation alter the diversity and function of soil bacterial and fungal communities, thereby causing an impact on agroecosystems.

Probiotic-enriched milk and dairy products increase gut microbiota diversity: a comparative study

Targeting gut microbiota with probiotics has emerged as a promising nutritional approach for the prevention of obesity and metabolic syndrome. Cultured dairy products can be effectively employed for the delivery of probiotics to the gut as well as for the support of growth and survival of probiotic bacteria. The purpose of this study was to characterize the effects of probiotic-enriched pasteurized milk and dairy products (Greek-style yogurt and cottage cheese) of different origins (cow, goat, and camel) on taxonomic composition of the mouse gut microbiota. We hypothesized that cultured dairy products can be an effective vector for the delivery of probiotics to the gut because of its nutritional value, acidic nature, and long shelf-life. Mice were fed a standard low fat, plant polysaccharide-rich (LF/PP) diet supplemented with the probiotic-enriched milk and dairy products for 5 weeks. Next generation sequencing of DNA from mouse fecal samples was used to characterize the bacterial relative abundance. Mice fed a diet supplemented with camel milk demonstrated characteristic changes in the gut microbiota, which included an increase in relative abundance of order Clostridiales and genus Anaerostipes. Mice fed a diet supplemented with the probiotic-enriched cow cheese exhibited an increase in the relative abundance of order Clostridiales, family Ruminococcaceae, and family Lachnospiraceae. The results obtained and their bioinformatics analysis support the conclusion that camel milk and the probiotic cow cheese induce changes in the mouse gut microbiota, which can be characterized as potentially beneficial to health compared to the changes associated with a standard diet. These findings imply that probiotic-enriched milk and dairy products can be highly effective for the delivery and support of probiotic bacteria of the gut.

Oral microbial dysbiosis and its performance in predicting oral cancer.

Dysbiosis of oral microbiome may dictate the progression of oral squamous cell carcinoma (OSCC). Yet, the composition of oral microbiome fluctuates by saliva and distinct sites of oral cavity and is affected by risky behaviors (smoking, drinking and betel quid chewing) and individuals' oral health condition. To characterize the disturbances in the oral microbial population mainly due to oral tumorigenicity, we profiled the bacteria within the surface of OSCC lesion and its contralateral normal tissue from discovery (n = 74) and validation (n = 42) cohorts of male patients with cancers of the buccal mucosa. Significant alterations in the bacterial diversity and relative abundance of specific oral microbiota (most profoundly, an enrichment for genus Fusobacterium and the loss of genus Streptococcus in the tumor sites) were identified. Functional prediction of oral microbiome shown that microbial genes related to the metabolism of terpenoids and polyketides were differentially enriched between the control and tumor groups, indicating a functional role of oral microbiome in formulating a tumor microenvironment via attenuated biosynthesis of secondary metabolites with anti-cancer effects. Furthermore, the vast majority of microbial signatures detected in the discovery cohort was generalized well to the independent validation cohort, and the clinical validity of these OSCC-associated microbes was observed and successfully replicated. Overall, our analyses reveal signatures (a profusion of Fusobacterium nucleatum CTI-2 and a decrease in Streptococcus pneumoniae) and functions (decreased production of tumor-suppressive metabolites) of oral microbiota related to oral cancer.

The clinical outcomes of medical therapies in chronic rhinosinusitis are independent of microbiomic outcomes: a double-blinded, randomised placebo-controlled trial.

Oral and topical corticosteroids, and antibiotics form the mainstay medical treatment of chronic rhinosinusitis (CRS). Clinical outcomes vary depending on the chosen therapy, resident microbiome and disease phenotype. We conducted a double- blinded, placebo-controlled Randomised Controlled Trial (RCT) to investigate effects of medical therapy on clinical outcomes and associated microbiome shifts. Fifty eligible patients (CRS with and without polyps) were treated for 3 weeks after randomisation into 3 arms: na- mely oral prednisolone, topical budesonide irrigations and oral doxycycline; each with appropriate placebo. Clinical scoring and microbiome swabs were performed on enrolment, at treatment completion and 3-weeks post treatment completion. Microbiome analysis was performed using the llumina-MiSeq next generation sequencing platform and QIME-2 pipeline. Significant improvement in clinical scores was observed in prednisolone and budesonide arms at treatment completion but not with antibiotic. Sub-group analysis showed more pronounced effects in patients with polyposis. Corynebacterium and Staphylococcus species predominated, with variable bacterial relative abundance among different treatments at all time-points. The only significant microbiome finding was an increase in bacterial diversity in topical budesonide group immediately after treatment, which returned to baseline 3-weeks post treatment. Clinical improvement was significant with oral and topical steroid but not empirical antibiotic. Although there were some associated microbiome changes with the various treatments, we could not ascertain the consistency of these and whether they do have a clinical significance at all.