Search

We aimed to investigate the effects of sodium alginate (SA) and galactooligosaccharides (GOS) on the metabolism and gut microbiota of high-fat diet (HFD)-fed obese mice. GOS and SA delayed high-fat diet-induced obesity, reduced the epididymal fat and liver indices, and improved the circulating lipid profile. Low- and high-dose GOS reduced weight gain by 48.8 % and 35.3 %, and low- and high-dose SA reduced it by 37.7 % and 34.4 %, respectively. GOS and SA reduced blood glucose concentration, probably by increasing the expression of glucose transporter 4. GOS and SA increased the expression of tight junction proteins (ZO-1 and occludin), reduced the D-lactic acid (D-LA) and lipopolysaccharide concentrations, and reduced the expression of toll-like receptors, consistent with improved intestinal barrier function. GOS and SA also increased the abundance of Bacteroidota, Bifidobacterium, and Lactobacillus; and reduced that of Patescibacteria in the gut. The abundance of Parabacteroides positively correlated with the circulating low-density lipoprotein-cholesterol (LDL-C) concentration; that of Lactobacillus negatively correlated with LDL-C, D-LA, and tumor necrosis factor-α concentration; and that of Bifidobacterium positively correlated with high-density lipoprotein-cholesterol concentration, according to Spearman correlation analysis. In conclusion, SA and GOS ameliorate obesity and the associated metabolic disorders in mice, and also modulate their gut microbial composition.

Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.

We analyzed the diversity of bacterial communities, metabolic activity, pH, and anthropogenic impact in the water of the estuaries and estuarine waters of the rivers in Southern Baikal in 2018 with different chemical composition. The chemical composition of waters and values of total microbial count (TMC), organotrophic bacteria (OB), and bacterial production (BP) depended on the geographical position, length of the rivers, and their water quality. In rivers with water acidification, we did not detect an effect of pH on TMC, abundance of OB, or total amount of mesophilic aerobic and facultative anaerobic microorganisms (PC). In rivers with a discharge of untreated domestic sewage, there was an increase in the content of dissolved organic carbon (DOC), concentration of nutrients, number of fecal and mesophilic bacteria, and high metabolic activity of microorganisms. The value of bacterioplankton production reached 0.26 to 12.41 per day−1; TMC – 0.155 ± 0.002 to 3.474 ± 0.044 million cells/mL. Using the massive parallel sequencing of fragments encoding the V2–V3 region of the 16S rRNA gene, we studied the diversity of bacteria and estimated the influence of chemical composition on the diversity of communities. As in other freshwater ecosystems and the pelagic zone of Lake Baikal, the members of freshwater Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Verrucomicrobia predominated in the estuaries and estuarine waters of the rivers. The obtained data on the number and diversity of hygiene indicator bacteria suggested fecal pollution of the rivers of Southern Baikal.

Background & Aims Fecal microbiota transplantation (FMT) is an emerging treatment modality for ulcerative colitis (UC). Several randomized controlled trials have shown efficacy for FMT in the treatment of UC, but a better understanding of the transferable microbiota and their immune impact is needed to develop more efficient microbiome-based therapies for UC. Methods Metagenomic analysis and strain tracking was performed on 60 donor and recipient samples receiving FMT for active UC. Sorting and sequencing of immunoglobulin (Ig) A–coated microbiota (called IgA-seq) was used to define immune-reactive microbiota. Colonization of germ-free or genetically engineered mice with patient-derived strains was performed to determine the mechanism of microbial impact on intestinal immunity. Results Metagenomic analysis defined a core set of donor-derived transferable bacterial strains in UC subjects achieving clinical response, which predicted response in an independent trial of FMT for UC. IgA-seq of FMT recipient samples and gnotobiotic mice colonized with donor microbiota identified Odoribacter splanchnicus as a transferable strain shaping mucosal immunity, which correlated with clinical response and the induction of mucosal regulatory T cells. Colonization of mice with O splanchnicus led to an increase in Foxp3+/RORγt+ regulatory T cells, induction of interleukin10, and production of short chain fatty acids, all of which were required for O splanchnicus to limit colitis in mouse models. Conclusions This work provides the first evidence of transferable, donor-derived strains that correlate with clinical response to FMT in UC and reveals O splanchnicus as a key component promoting both metabolic and immune cell protection from colitis. These mechanistic features will help enable strategies to enhance the therapeutic efficacy of microbial therapy for UC. Clinicaltrials.gov ID NCT02516384 .

Vaginal microenvironment plays a significant role in bovine fertility since its resident microorganisms interact with the host mucosa and constitutes the first barrier against ascending pathogens in the reproductive tract. In this study, the vaginal microbiome of healthy heifers (H) and cows with impaired reproductive performance, metritis complex (MT) or repeat breeders (RB), was assessed using a 16S rRNA gene sequencing approach. Analysis revealed that even though a vaginal microbiological guild (Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes, Fusobacteria and Actinobacteria) was shared among healthy heifers and cows with uterine disease; further analysis at genus level showed significant differences depending on the reproductive health status. The relative abundances of recognized uterine pathogens such as Bacteroidetes, Fusobacterium and Helcococcus were higher in MT when compared with H and RB; therefore, their presence in vagina can be considered as a risk factor for fertility. The present study describes for the first time, the composition of native bacterial communities in the vagina of cows undergoing the repeat breeding syndrome (RBS), and reports an association between this disease and the presence of Porphyromonas and unassigned genera of the Pasteurellaceae family. In addition, this work highlights the bacteria associated with a healthy vagina: genera from the families Lachnospiraceae, Rikenellaceae and the genera Acinetobacter, Bacillus, Oscillospira, CF231 and 5-7NS. Results highlighted herein, signify the potential of the evaluation of the bovine vaginal microbiome to future design therapeutic interventions to improve pregnancy rates however, further research is needed to elucidate the balance of bacterial species resulting in an optimal reproductive health.

The highly diverse nature of plant microbiota is indicative of many ecological roles of this group of microorganisms. For important medicinal plants such as Artemisia annua L (Family Asteraceae), there can be numerous functional attributes of the associated bacterial endophytes, but the diversity and functions of such endophytes remain widely unknown. To understand their potential functional diversity, we isolated endophytic bacteria associated with the plant from different plant parts including leaves, stems, and roots. Bacterial community of the leaves showed more diversity than those of the stems and the roots. Bacterial isolates were screened in vitro for various plant growth promoting attributes including Indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase production, and nitrogen fixation. Ninety five percent of the isolates were able to produce IAA, while 7.5% produced ACC deaminase, and 15% were able to fix nitrogen. Based on their potential plant growth promoting attributes, 25 bacterial isolates of 16 genera belonging to four phyla were identified. Proteobacteria (36%) and Firmicutes (36%) were the most predominant isolated bacteria, followed by Actinobacteria (24%) and Bacteroidetes (4%). The most promising isolates were selected for the investigation of their ability to enhance seed germination. We observed that the treatment with isolates AAR80 Bacillus selenatarsenatis and AAL56 Achromobacter xylosoxidans increased germination percentage of inoculated seeds. Moreover, (48%) of the isolates showed antimicrobial activity upon testing against indicator microorganisms. This study revealed that endophytic bacteria isolated from A. annua L have dual potential to be used as growth promoters and antimicrobial agents.

Enterocytozoon bieneusi is a common gastrointestinal parasite that has a broad range of hosts, including birds, mammals, and even humans. The changes of gut bacterial communities have been demonstrated during the course of E. bieneusi. This study aimed to examine the infection status, and assess the zoonotic potential and influence of E. bieneusi on gut bacterial communities of captive foxes in Xinxiang, central China. Fecal samples were collected from 216 captive foxes, and amplification of the internal transcribed spacer (ITS) gene of each sample was performed by nested polymerase chain reaction. E. bieneusi was detected in 48 (22.2%) samples, and five previously reported genotypes CHN-F1 (n = 25), D (n = 18), BEB6 (n = 3), NCF2 (n = 1), and CHN-DC1 (n = 1) were identified, with CHN-F1 being the dominant genotype (25/48, 52.1%). Phylogenetic analysis further revealed that CHN-F1, D, NCF2, and CHN-DC1 genotypes belonged to the zoonotic group 1 of E. bieneusi, whereas BEB6 belonged to group 2. Moreover, sequencing and bioinformatics analysis of the V3–V4 region of 16S rRNA gene in five E. bieneusi-positive and five negative samples showed that gut microbial diversity was higher in the infected animals. In both groups, Firmicutes and Bacteroidetes were the two most abundant phyla, but the Firmicutes/Bacteroidetes ratio was lower in E. bieneusi-positive foxes (7.9:1) as compared with E. bieneusi-negative foxes (5:1). More importantly, at the phylum level, “beneficial bacteria” such as Firmicutes (1.6%) and Bacteroides (5.8%) increased, whereas “opportunistic pathogens” such as Fusobacteria (8.2%) decreased. Similarly, at the genus level, the pathogenic Clostridiaceae_Clostridium (10.0%) decreased, whereas the “beneficial bacteria” Lactococcus (6.6%) increased. These interesting phenomena warrant further investigation.

Chronic disruption of rhythms (CDR) impacts sleep and can result in circadian misalignment of physiological systems which, in turn, is associated with increased disease risk. Exposure to repeated or severe stressors also disturbs sleep and diurnal rhythms. Prebiotic nutrients produce favorable changes in gut microbial ecology, the gut metabolome, and reduce several negative impacts of acute severe stressor exposure, including disturbed sleep, core body temperature rhythmicity, and gut microbial dysbiosis. In light of previous compelling evidence that prebiotic diet broadly reduces negative impacts of acute, severe stressors, we hypothesize that prebiotic diet will also effectively mitigate the negative impacts of chronic disruption of circadian rhythms on physiology and sleep/wake behavior. Male, Sprague Dawley rats were fed diets enriched in prebiotic substrates or calorically matched control chow. After 5 weeks on diet, rats were exposed to CDR (12 h light/dark reversal, weekly for 8 weeks) or remained on undisturbed normal light/dark cycles (NLD). Sleep EEG, core body temperature, and locomotor activity were recorded via biotelemetry in freely moving rats. Fecal samples were collected on experimental days –33, 0 (day of onset of CDR), and 42. Taxonomic identification and relative abundances of gut microbes were measured in fecal samples using 16S rRNA gene sequencing and shotgun metagenomics. Fecal primary, bacterially modified secondary, and conjugated bile acids were measured using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Prebiotic diet produced rapid and stable increases in the relative abundances of Parabacteroides distasonis and Ruminiclostridium 5. Shotgun metagenomics analyses confirmed reliable increases in relative abundances of Parabacteroides distasonis and Clostridium leptum, a member of the Ruminiclostridium genus. Prebiotic diet also modified fecal bile acid profiles; and based on correlational and step-wise regression analyses, Parabacteroides distasonis and Ruminiclostridium 5 were positively associated with each other and negatively associated with secondary and conjugated bile acids. Prebiotic diet, but not CDR, impacted beta diversity. Measures of alpha diversity evenness were decreased by CDR and prebiotic diet prevented that effect. Rats exposed to CDR while eating prebiotic, compared to control diet, more quickly realigned NREM sleep and core body temperature (ClockLab) diurnal rhythms to the altered light/dark cycle. Finally, both cholic acid and Ruminiclostridium 5 prior to CDR were associated with time to realign CBT rhythms to the new light/dark cycle after CDR; whereas both Ruminiclostridium 5 and taurocholic acid prior to CDR were associated with NREM sleep recovery after CDR. These results support our hypothesis and suggest that ingestion of prebiotic substrates is an effective strategy to increase the relative abundance of health promoting microbes, alter the fecal bile acid profile, and facilitate the recovery and realignment of sleep and diurnal rhythms after circadian disruption.

The toxic effect of dietary histamine on the intestine of aquatic animals has been demonstrated, but reports on the morphological observation of the intestine are limited. Thus, a feeding trial was conducted to determine the effect of dietary histamine on intestinal histology, inflammatory status and gut microbiota of yellow catfish (Pelteobagrus fulvidraco). Here, we showed that histamine-rich diets caused severe abnormality and damage to the intestine, including a decreased villi length and reduced villi number. In addition, the quantitative real-time PCR (qRT-PCR) demonstrates that histamine-rich diets increased the expression of pro-inflammatory genes (Tnfα, Il1β, and Il8) and decreased the expression of an anti-inflammatory gene (Il10). Furthermore, the alpha-diversity (observed OTUs, Chao1, Shannon and Simpson) and beta-diversity (non-metric multidimensional scaling, with the stress value of 0.17) demonstrated that histamine-rich diets caused alterations in gut microbiota composition and diversity. Co-occurrence networks analysis of the gut microbiota community showed that the histamine influenced the number and the relationship between bacteria species in the phyla of Acidobacteria, Proteobacteria, and Bacteroidetes, which caused the instability of the intestinal microbiota community. Additionally, random forest selected six bacterial species as the biomarkers to separate the three groups, which are Lachnospiraceae Blautia (V520), Bacteroidales S24.7 (V235), Chloroplast Streptophyta (V368), Actinomycetales Streptomycetaceae (V152), Clostridia Clostridiales (V491) and Paraprevotellaceae Prevotella (V245). Finally, Pearson correlation analysis demonstrated that V520, V235, and V491 were negatively correlated with pro-inflammatory factors (Tnfα, Il1β, and Il8) and positively correlated with an anti-inflammatory factor (Il10), which indicated that V520, V235, and V491 might be anti-inflammatory. These findings improved our understanding of the toxic effect of dietary histamine to intestinal histological damage, the induction of mucosa inflammatory status, and the alteration of gut microbiota.

Background: Weight loss and decline of milk yield in Tibetan sheep was a challenge for the dairy industry in Qinghai-Tibet Plateau, which were considered to be caused by underfeeding of the sheep during the harsh winter. The objective of this study was to assess the role of feed supplementation in the milk performance and rumen microbiome of ewes under forage-based diets. Based on parity, milking period, milk yield, and body weight, ten 1.5-yr-old ewes were allocated randomly into two groups. One group of ewes was fed no supplement Control group (CON) and the other group was fed with concentrate feed supplement (Treatment group, T). Individual milk yield was determined daily; both the milk composition and rumen bacterial characteristics were analyzed after the end of feeding trials. Results: Results showed that lactose in the milk of the CON group was significantly lower (P

BACKGROUND: Gastrointestinal dysfunction is a frequent and disabling manifestation of autoimmune polyendocrine syndrome type 1 (APS-1), a rare monogenic multi-organ autoimmune disease caused by the loss of central AIRE-controlled immune tolerance. OBJECTIVE: We aimed to understand the role of the gut microbiome in APS-1 symptoms and potentially alleviate common gastrointestinal symptoms by probiotic intervention. METHODS: We characterized the fecal microbiomes of 28 APS-1 patients and searched for associations with gastrointestinal symptoms, circulating anti-cytokine autoantibodies and tryptophan-related metabolites. We additionally administered daily doses of the probiotic Lactobacillus rhamnosus GG for three months. RESULTS: Of 581 metagenomic operational taxonomic units (mOTUs) characterized in total, 14 were significantly associated with APS-1 compared to healthy controls, with six mOTUs depleted and eight enriched in APS-1 patients. Four overabundant mOTUs were significantly associated with severity of constipation. We observed phylogenetically conserved microbial associations with autoantibodies against cytokines. After the three-month intervention with the probiotic L. rhamnosus GG, a subset of gastrointestinal symptoms were alleviated. L. rhamnosus GG abundance was increased post-intervention and corresponded with decreased abundances of Alistipes onderdonkii and Collinsella aerofaciens, two species positively associated with severity of diarrhea in APS-1 patients. CONCLUSION: The APS-1 microbiome correlates with several APS-1 symptoms, some of which are alleviated after a three-month L. rhamnosus GG intervention. Autoantibodies against cytokines appear to shape the gut microbiome by positively correlating with a taxonomically consistent group of bacteria. CLINICAL IMPLICATIONS: Administration of L. rhamnosus GG appears to alleviate certain gastrointestinal symptoms of APS-1.

This study investigated the effects of floor and cage rearing systems on performance, meat quality, and enteric microorganisms of male and female yellow feather broilers. Two hundred Xueshan chickens (42 days old; 100 of each sex) were divided into four groups, according to sex and rearing system (stainless-steel cage or litter floor). Male and cage-reared broilers exhibited better (P0.05) by rearing system. The enteric microbiota assessment by 16S rRNA amplicon-based sequencing showed that Firmicutes, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both rearing systems, and that the cecum was relatively stable in terms of microbiome composition. Floor-reared broilers exhibited a richer diversity of bacteria in the intestinal tract than cage-reared broilers, while alpha diversity was not significantly different (P>0.05) among the groups. The ratio of Bacteroidetes to Firmicutes and the abundance of Helicobacter and Romboutsia could potentially affect the production of broilers. These findings indicate that cage rearing improved the production of male Xueshan broilers, which may be due to the difference in enteric microbiota between cage and floor rearing systems.

Like many seemingly inhospitable environments on our planet, the highly acidic human stomach harbors a diverse bacterial microflora. The best-known member of the human gastric flora, Helicobacter pylori, causes a number of gastric diseases, including peptic ulcer disease and gastric adenocarcinoma. In the absence of Helicobacter pylori infection, the gastric microbiota displays some features similar to the oral cavity with Firmicutes the most common phylum, followed by Proteobacteria and Bacteroidetes. When present, H. pylori dominates the gastric microbiome and reduces diversity and composition of other taxa. The composition of the gastric microbiome also is altered in the setting of proton pump inhibitor therapy and gastric neoplasia. This review summarizes foundational and recent studies that have investigated the composition of the human gastric microbiome in a variety of patient groups, with a focus on potential mechanisms involved in regulation of gastric microbial community structure.

Numerous studies have evaluated the toxicity and endocrine disrupting properties of organic UV filters for aquatic organisms, but little is known about their biodegradation in river sediments and their impact on microorganisms. We have set up the sterile and microbiological systems in the laboratory, adding 2-ethylhexyl-4-methoxycinnamate (EHMC), one of organic UV filters included in the list of high yield chemicals, at concentrations of 2, 20 and 200 μg/L, and characterized the microbial community composition and diversity in sediments. Monitoring of EHMC degradation within 30 days revealed that the half-life in the microbial system (3.49 days) was much shorter than that in the sterile system (7.55 days). Two potential degradation products, 4-mercaptobenzoic acid and 3-methoxyphenol were identified in the microbial system. Furthermore, high-throughput 16s and 18s rRNA gene sequencing showed that Proteobacteria dominated the sediment bacterial assemblages followed by Chloroflexi, Acidobacteria, Bacteroidetes and Nitrospirae; Eukaryota_uncultured fungus dominated the sediment fungal assemblages. Correlation analysis demonstrated that two bacterium genera (Anaerolineaceae_uncultured and Burkholderiaceae_uncultured) were significantly correlated with the biodegradation of EHMC. These results illustrate the biodegradability of EHMC in river sediments and its potential impact on microbial communities, which can provide useful information for eliminating the pollution of organic UV filters in natural river systems and assessing their potential ecological risks.

The composition of the gastrointestinal microbiota is associated with obesity. We hypothesized that the gut microbiota influences the outcomes of bariatric surgery.We aimed to analyze using oral swabs and stool samples the microbiota of patients with morbid obesity who were undergoing laparoscopic sleeve gastrectomy (SG).A university hospital in Poland.This prospective cohort study was conducted between November 2018 and June 2019. Participants underwent SG or no surgery (controls). Results were then analyzed as a group 1 (surgical participants who achieved a percentage of excess weight loss [%EWL]50%), group 2 (surgical participants who achieved a %EWL50%), and group 3 (nonsurgical controls). %EWL was measured 6 months following surgery. Before surgery, oral swabs were obtained and stool samples were provided. The endpoint was the composition of the gut microbiota.Group 1 comprised 19 participants, group 2 comprised 11 participants, and group 3 comprised 16 participants. No participants were lost to follow-up during the study. Participants in group 1 had an oral microbiota that was enriched in the phyla Proteobacteria, and Bacteroidetes. Their intestinal microbiota was enriched in the Proteobacteria. In contrast, the oral microbiota of group 2 was enriched in the Actinobacteria and the intestinal microbiota was enriched in the phyla Bacteroidetes and Firmicutes.The compositions of the microbiota of the oral cavity and large intestine are related to the weight loss achieved following SG.

Pea starches, in both native (NPS) and retrograded-autoclaved forms (RAPS), were subjected to simulated gastrointestinal (GI) digestion in vitro, their multi-scale structural characteristics, morphological features, molecular distribution and thermal properties were characterized. A gradual increase in the short−/long-range crystallinity, melting enthalpy of gelatinization on increasing digestion time was observed for both the native and retrograded-autoclaved pea starch samples based on the X-ray diffraction, Fourier-transform infrared spectra, solid-state 13CNMR and differential scanning calorimetry measurements. It was especially noticed that the growth rate of crystallinity and double helices, as well as the decrease in Mw values were evidently greater for RAPS than for NPS. To investigate how different molecular fine structure of pea starch substrate affects the gut microbiota shifts and dynamic short-chain fatty acid profile, their resistant starch residues obtained from both native and retrograded-autoclaved pea starch after 8 h of simulated GI tract digestion was used as the fermentation substrate. The levels of acetate, propionate and butyrate gradually increased with the increasing fermentation time for NPS and RAPS. In comparison to the blank control (i.e., the group without the addition of carbohydrate), the fermented NPS and RAPS obviously resulted in an increased abundance of Firmicutes and Bacteroidetes, accompanied by a decrease in Proteobacteria, Actinobacteria and Verrucomicrobia. Both NPS and RAPS promoted different shifts in the microbial community at the genus level, with an increase in the abundance of Bacteroides, Megamonas and Bifidobacterium, as well as a reduction in the abundance of Fusobacterium, Faecalibacterium and Lachnoclostridium in comparison to the blank control samples.

BACKGROUND: Bacterial exposure from house dust has been associated with asthma and atopy in children but whether these relationships are present in adults remains unclear. OBJECTIVE: To examine associations of house dust microbiota with adult asthma, atopy, and hay fever. METHODS: Vacuumed bedroom dust samples from the homes of 879 participants (average age 62) in the Agricultural Lung Health Study, a case-control study of asthma nested within a farming cohort, were subjected to 16S rRNA amplicon sequencing to characterize bacterial communities. We defined current asthma and hay fever using questionnaires and current atopy by blood specific immunoglobulin E > 0.70 IU/ml to ≥ 1 of ten common allergens. We used linear regression to examine whether overall within-sample bacterial diversity differed by outcome, microbiome regression-based kernel association test (MiRKAT) to evaluate whether between-sample bacterial community compositions differed by outcome, and analysis of composition of microbiomes (ANCOM) to identify differentially abundant bacterial taxa. RESULTS: Overall diversity of bacterial communities in house dust was similar by asthma status but was lower (p-value < 0.05) with atopy or hay fever. Many individual bacterial taxa were differentially abundant (false discovery rate < 0.05) by asthma, atopy, or hay fever. Several taxa from Cyanobacteria, Bacteroidetes, and Fusobacteria were more abundant with asthma, atopy, or hay fever. In contrast, several taxa from Firmicutes were more abundant in homes of individuals with adequately controlled asthma (vs inadequately controlled asthma), non-atopics, or individuals without hay fever. CONCLUSION: Microbial composition of house dust may influence allergic outcomes in adults.

An artificial-natural coupled wetland was constructed at an estuary between an upstream river and a downstream lake to transport river water and reduce nutrient input load into a grass-type shallow lake. The removal efficiencies of chemical oxygen demand (COD) and total nitrogen (TN) were as high as 43 % and 83 %, respectively. Their concentrations were reduced to 30.98 mg/L and 0.79 mg/L, respectively. The lotus pond had high microbial diversity and was key for water purification. It contributed 19 % and 49 % of the removal efficiencies of COD and TN, respectively. Most of the dominant microorganism in wetland were related to the transformation of C and N. Bacterial phyla containing phototrophic members accounted for three-quarters of the microorganisms and significantly contributed to bioactivity. Phylum Proteobacteria, the most abundant microbial species, were involved in both N and C cycling because of the metabolic versatility. The denitrification of the wetland depended on the classes Gammaproteobacteria, Deltaproteobacteria, Bacteroidia and Anaerolineae. Bacteria of the phyla Chloroflexi, Actinobacteria, Firmicutes, Spirochaetes, Bacteroidetes and class Alphaproteobacteria contributed to hydrocarbon mineralization and carbonate decomposition to promote C cycling. Therefore, this study provides insights to develop effective methods for reducing the risks of lake eutrophication and protecting the water ecological health.

To address concerns about the biocompatibility of novel phenolic immobilization-based food preservatives, their impact on the composition and metabonomic profile of a defined community of human gut microbiota was evaluated. Three phenolics (eugenol, vanillin and ferulic acid) presented in two forms (free or immobilized on different supports) were tested at two concentration levels (0.5 and 2 mg/mL). Free eugenol was the phenolic with the greatest impact on gut microbiota, with a remarkable increase in the abundance of Lachnospiraceae and Akkermansiaceae families. In contrast, immobilized phenolics produced an increase in the abundance of Bacteroides with a reduction in the ratio of Firmicutes to Bacteroidetes. The metabonomic profile was also affected by free and immobilized phenolics differently in terms of fermentation by-products and phenolic biotransformation metabolites. Thus the results suggest the importance of evaluating the impact of new compounds or materials added to food on human gut microbiota and their potential use to modulate microbiota composition.

It was our hypothesis that foods high in polyphenols and fiber have prebiotic activity. This human intervention study aimed to determine if daily consumption of freeze-dried California strawberry powder (SBP) leads to changes in the intestinal microbiota, fecal cholesterol and bile acid (BA) microbial metabolites. Fifteen healthy adults consumed a beige diet+26 g of SBP for 4 weeks, followed by 2 weeks of beige diet only. Stool samples were collected at 0, 4, and 6 weeks. Fecal microbiota was analyzed by 16S rRNA sequencing; fecal cholesterol, BA, and microbial metabolites by gas chromatography. Confirming compliance, urine concentration of pelargonidin, urolithin A glucuronide and dimethylellagic acid glucuronide were present after 4 weeks of SBP consumption. Daily SBP altered the abundance of 24 operational taxonomic units (OTUs). Comparing week 4 to baseline the most significant increases were observed for one OTU from Firmicutes\Clostridia\ Christensenellaceae\NA, one OTU from Firmicutes\ Clostridia\Mogibacteriacea\NA, one OTU from Verrucomicrobia\ Verrucomicrobiaceae\Akkermansia\Muciniphila, one OTU from Actinobacteria\ Bifidobacteriaceae\Bifidobacterium\NA, and one OTU from Bacteroidetes\Bacteroidia\ Bacteroidaceae\Bacteroides and decrease of one OTU from Proteobacteria\ Betaproteobacteria\Alcaligenaceae\Sutterella. Comparing week 4 to 6, we observed a reversal of the same OTUs from C Christensenellaceae, V muciniphilia and C Mogibacteriaceae. Fecal short chain fatty acids and most of the fecal markers including cholesterol, coprostanol, primary and secondary BAs were not changed significantly except for lithocholic acid, which was increased significantly at week 6 compared to baseline. In summary, SBP consumption increased the abundance of gut microorganisms related to lean body weight, health and longevity, and increased fecal lithocholic acid at week 6 in healthy study participants.

The in vitro digestive and fermentation properties of Sargassum pallidum polysaccharide (SPP) after ultrasound degradation were investigated. The results showed that SPP and its degraded fractions were not affected by human saliva, but slightly degraded by breaking glycosidic bonds under simulated gastrointestinal digestion. The DPPH radical scavenging activity, α-glucosidase inhibitory activity, and bile acid-binding capacity of SPP and its degraded fractions were decreased after digestion, which was attributed to the reduction of molecular weights (MWs) and viscosity. Furthermore, in vitro fermentation assay indicated that SPP and its degraded fractions showed good fermentability. The predominant compositional monosaccharides including arabinose, galactose, glucose, xylose, and uronic acid were significantly decreased, and the degraded SPP fractions were more easily fermented and utilized by gut bacteria. SPP and its degraded fractions could modulate gut health by decreasing the Firmicutes/Bacteroidetes ratio and increasing the relative abundances of some beneficial genera, such as Prevotella, Dialister, Phascolarctobacterium, Ruminococcus, and Bacteroides. These findings suggested that SPP and its degraded fractions exhibited similar influence on gut microbiota community, but appropriate degraded SPP fractions were more easily fermented by gut microbiota.

The biogas slurry produced by anaerobic fermentation process contained a large amount of dissolved organic matter (DOM). In this study, the reason for the effect of sulfanilamide antibiotics (SAs) on DOM components was revealed by analyzing the interaction between microbial community structure and DOM composition in the biogas slurry. Four components of DOM, including tyrosine-like, tryptophan-like or xenobiotic-like, Ultraviolet A (UVA) humic-like and UVA marine humic-like substances, were identified from all the samples through fluorescence excitation emission matrix-parallel factor (EEM-PARAFAC) analysis. The most abundant phyla in biogas slurry were identified to be Firmicutes (60.99 %), Bacteroidetes (19.65 %), Proteobacteria (15.33 %) and Actinobacteria (3.15 %). The contents of soluble microbial byproduct-like substances were related to the growth and metabolism of high abundance of bacterial phyla. Firmicutes could lead to the content change of tyrosine-like substance. The content of the xenobiotic-like substance was negatively correlated with the abundances of Bacteroidetes and Proteobacteria. The addition of high concentration SAs inhibited the growth and reproduction of Firmicutes, resulting in the decrease of the content of tyrosine-like substance. The addition of 100 mg/L sulfaquinoxaline and sulfamethoxydiazine reduced the content of tyrosine-like by 47.5 % and 41.2 %, respectively. The change of tryptophan-like groups was opposite to that of the tyrosine-like. However, the addition of sulfamethoxazole had little effect on the content of all the abovementioned substances.

The structure and molecular dynamics of α-L-arabinofuranosidase (PsGH43_12) of family 43 glycoside hydrolase, subfamily 12 from Pseudopedobacter saltans were studied. The modeled PsGH43_12 structure displayed 5-bladed β-propeller fold at N-terminal and β–sandwich fold at C terminal. Ramachandran plot showed 95.7% residues in favored and 3.3% in the generously allowed region and only 1% residues in the disallowed region. The secondary structure analysis of PsGH43_12 by circular dichroism revealed 2.7% α-helices, 30.33% β-strands and 66.97% random coils. Protein melting study of PsGH43_12 showed complete unfolding at 65°C and did not require any metal ion for its stability. Molecular docking analysis confirmed the involvement of active site residues Asp71, Asp180 and Glu247 in the catalysis, which was also confirmed by the site-directed mutagenesis of these residues. SAXS analysis displayed that PsGH43_12 is monomeric and a fully folded state in solution form. Guinier analysis gave the radius of gyration (Rg) 2.8 ± 0.09 nm. The maximum dimension and Rg of PsGH43_12 estimated from P(R) plot were 9.7 nm and 2.81 nm, respectively. The ab initio derived dummy model of PsGH43_12 displayed a bell-like shape. The ab initio derived dummy model superposed well with its comparative modeled structure except the N-terminal His6-tag region.

Endophytes mainly present in the tissues of the plants. The effects of endophytes on host physiology and ecology have been relatively well studied in many plants, while the functions of endophytes within invasive plants are few that have been reported. Endophytic bacteria considered mutualistic and mediate nutrients availability to facilitate the growth and competitiveness of the host. The present study aimed to check how alien plant species have positive population growth and to identify the functional gene diversities of endophytic bacteria in the tissues. An alien plant, Ageratina adenophora has been experimentally manipulated in order to investigate the bacterial community structure of endophytes in its roots, stems and leaves. Results indicated that after tetracycline treatment, the heights of A. adenophora plants were significantly reduced. Several changes in the host physiological and biochemical properties were detected, including decreased ferredoxin contents, increased iron and chlorophyll concentrations in the leaves. High-throughput sequencing of the bacterial community 16S rRNA genes indicated that endophytic bacteria in untreated A. adenophora plants were dominated by the phyla Cyanobacteria, Proteobacteria, Firmicutes and Bacteroidetes. After treatment with tetracycline, the overall bacterial diversity decreased. To investigate the links between endophytic bacteria and host growth, six strains of bacteria (Acinetobactor johnsonii, Chryseobacterium arthrosphaerae, Bacillus sp., Arthrobacter nitroguajacolicus, Bacillus cereus and an unidentified bacterium sp.) were isolated from A. adenophora. Three of these isolates produced indole-3-acetic acid, which has been shown to promote the growth of A. adenophora plants. These strains also showed strong nematicidal activities, suggesting their potential roles in aiding host defense mechanisms.

Background Low microbial diversity or altered microbiota composition is associated with many disease states. In the treatment of many conditions, enteral (EN) or parenteral (PN) nutrition is frequently required. Objective This systematic review aimed to identify and evaluate the evidence of the effect of EN vs PN on the gastrointestinal microbiota. Method A comprehensive systematic literature search of 5 databases was completed to review studies published until February 2020. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were utilized in completion of the review with the Academy of Nutrition and Dietetics quality criteria checklist and Grading of Recommendations Assessment, Development and Evaluation to evaluate the included studies. The review was registered on PROSPERO (CRD42018091328). Studies were eligible for inclusion if participants were older than 3 years, patients received either EN, PN or both, with some patients receiving each mode of nutrition support. The main outcome was any assessment of the gastrointestinal microbiota, including diversity or taxa abundance. Results Eleven articles (n = 367 patients) met the inclusion criteria and were evaluated. Seven studies (n = 237) reported greater abundance of Proteobacteria with the provision of PN compared to EN; 6 studies (n = 172) reported lower Firmicutes and 5 studies (n = 155) lower Bacteroidetes. In 7 studies (n = 282), microbial diversity was lower with provision of PN than EN. The Grading of Recommendations Assessment, Development and Evaluation certainty of evidence was very low. Conclusions Provision of PN may lead to greater abundance of Proteobacteria and reduced microbial diversity; however, there is limited literature on this topic and additional research is warranted to improve understanding of the impact of EN vs PN on the microbiota.

Salinity stress during anaerobic digestion is known to cause extensive changes in biogas production and microbial community structure. Thus, our study sought to characterize the adaptation response of bacteria when challenged with increased salinity. Firstly, experiments were conducted at eight salinity levels at a constant kitchen waste/inoculum ratio (K/I = 1.0), which indicated that the effect of salinity on anaerobic digestion was strictly dosage-dependent. Then, kitchen waste anaerobic digestion was conducted for 70 days at five increasing salinity levels (1.0, 2.0, 4.0, 8.0, and 16.0 g NaCl/g). Furthermore, six samples taken at the end of each salinity level acclimation phase were analyzed by high-throughput sequencing, which illustrated that Euryarchaeota, Synergistetes, Firmicutes, and Bacteroidetes were dominance at phylum level. Moreover, the proportion of Methanosaeta as major genus among Euryarchaeota was 16.46% after being acclimated 70 days of NaCl acclimation, which was higher than its proportions at the initial sample (22.08%). Methanosarcina were also enriched after acclimation. Therefore, Methanosaeta and Methanosarcina could both potentially adapt to high-salinity environments.

This study used microbial rDNA sequencing for accurate detection of systemic lupus erythematosus (SLE) skin lesions. 20 lupus erythematosus dermatology patients and 20 healthy persons were selected as experimental group and control group. Feces and serum of the subjects were sampled in sterile environment. Serum samples were examined for anti dsDNA antibodies. Fecal samples were analyzed by 16 s rDNA high-throughput sequencing, using Illumina MiSeq 2 × 250 sequencing platform. The results suggested that positive rate of anti-dsDNA antibody in serum was significantly higher in the experimental group than the control group. Significant difference of intestinal microbiome was spotted between the two groups in phylum (Firmicutes, Bacteroidetes) and genus level (Lactobacillus, Allobaculum, Lachnospira, Turicibacter, Bifidobacterium). The different intestinal microbiomes existing in healthy people and patients can provide a strong tool for accurate diagnose of lupus erythematosus.

It is generally accepted that domestic ducks are valuable protein sources for humans. The gastrointestinal ecosystem contains enormous and complicated microbes that have a profound effect on the nutrition, immunity, health, and production of domestic ducks. To deeply understand the gastrointestinal microbial composition of domestic ducks, we investigated the microbiomes of 7 different gastrointestinal locations (proventriculus, gizzard, duodenum, jejunum, ileum, cecum, and rectum) and the short-chain fatty acids in 15 healthy muscovy ducks based on 16S rRNA gene sequencing, qPCR, and gas chromatography. As a result, 1 029 735 sequences were identified into 35 phyla and 359 genera. Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria were the major phyla, with Bacteroidetes being most abundant in the cecum. The population of the total bacteria and the representatives of the Firmicutes, Bacteroidetes, and Bacteroides groups increased from the proximal to the distal part of the GIT. Bacteroides was the most dominant group in the cecum. Acetate, propionate, and butytrate, as well as gene copies of butyryl-CoA including acetate-CoA transferase and butyrate kinase, were significantly higher in cecum than in other sections. Isobutyrate, valerate, and isovalerate were only found in the cecum. The differences of microbial composition and the short-chain fatty acids of their metabolites among these 7 intestinal locations might be correlated with differences in gut function. All these results provide a reference for the duck gastrointestinal microbiome and a foundation for understanding the types of bacteria that promote health and enhance growth performance and decrease instances of disease in duck breeding.

The haze phenomenon in China gradually spreads from the north to the central and south areas. Changsha is the representative city in the central south region of China. In this study, we investigated the microorganism community structure of the different airborne particulate matter during hazy and nonhazy days in Changsha by the high throughput sequencing technology. The results show that the diversity of atmosphere microorganism community will increase with the increase of PM fraction and air quality index (AQI). In phylum level, Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes and Cyanobacteria are the dominant community members in ChangSha. In genera level, in the haze days the dominant community members were Rhodococcus (25.13%) and Staphylococcus (8.14%) for coarse particle (>2.5 μm), and Methylobacterium (25.84%) and Massillia (13.14%) for fine particle (

Bioregenerative Life Support System (BLSS) is a closed artificial ecosystem and could provide oxygen, food, water and other substances for space survival. Solid waste treatment is a key rate-limiting step in BLSS. In this study, solid wastes including wheat straw, human and yellow mealworm feces were disposed in a semi-continuous bio-convertor for 105 days in a ground-based experimental BLSS platform (Lunar Palace 1). Solid wastes at different periods were sampled and the microbial community variation, functional genes and metabolic pathways were analyzed. The results showed phyla Firmicutes, Bacteroidetes and Proteobacteria predominated in all samples. While microbial community structures at genus level were significantly different, indicating selective enrichment during the 105-day process. The abundance of functional gene related to carbohydrate transport and metabolism was predicted higher on 45-day and 70-day. The metabolic pathway analysis revealed the degradation mechanisms and provided evidence for metabolic regulation.

The host-associated gut microbiota is considered critical for the occurrence and progression of colorectal cancer (CRC); however, systematic evaluations of the changes in the biodiversity and richness of mucosa-associated gut microbiota with the development of CRC have been limited. Twenty-three paired samples from colorectal tumor sites and the surrounding non-tumor tissues were collected from stage I to IV CRC patients. The microbial compositions of the samples were analyzed by Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene. Gut bacterial alterations at the tumor sites and surrounding healthy tissue sites collected from the different stages of CRC patients were analyzed. No significant differences were observed in the overall microbial richness and biodiversity between the CRC tissue and surrounding non-CRC tissue samples, however, composition and community segregation of the gut microbiota with the progression of CRC were observed. A general increasing trend of Bacteroidetes, Firmicutes, and Fusobacteria and decreasing trend of Proteobacteria were observed at the phylum level with the development of CRC. Further analysis revealed that thirty-four taxa differed significantly with the progression of CRC. Conclusively, our findings provide a comprehensive view of the human mucosa-associated gut microbiota, in association with the different stages of CRC.

Small diameter gravity sewers (SDGS) are extensively used to collect rural sewage as they are low in cost and quick to construct. However, the characteristics of biofilms in rural SDGS are still not clear. In this study, biofilms characteristics of aerobic rural SDGS were investigated using simulations in a lab under different flow conditions and slopes. Results indicated that the average thickness of aerobic rural SDGS biofilms was in the range of 350–650 μm, decreasing at locations with variable flow and high slopes. Protein was the most abundant substance in extracellular polymeric substance of SDGS biofilms. The most abundant bacteria, Proteobacteria, Actinobacteria, and Bacteroidetes, and functional bacteria showed different distributions when analyzed through Illumina HiSeq sequencing of 16S rRNA. The relative abundances of denitrifying bacteria, nitrite-oxidizing bacteria, and sulfate-reducing bacteria (SRB) were lower during variable flow than during stable flow. High slopes (15‰) decreased SRB presence, which could be used to mitigate H2S accumulation in aerobic SDGS. Overall, this study describes the characteristics of aerobic rural SDGS biofilms and provides valuable suggestions for the optimal design of SDGS based on these characteristics.

To correctly assess and properly manage the public health risks associated with exposure to contaminated water, it is necessary to identify the source of fecal pollution in a watershed. In this study, we evaluated the efficacy of our two previously developed real time-quantitative PCR (qPCR) assays for the detection of swine-associated Bacteroidales genetic markers (gene 1-38, gene 3-53) in the Yangtze Delta watershed of southeastern China. The results indicated that the gene 1-38 and 3-53 markers exhibited high accuracy (92.5%, 91.7% conditional probability, respectively) in detecting Bacteroidales spp. in water samples. According to binary logistic regression (BLR), these two swine-associated markers were well correlated (P 0.05) with fecal indicators (Escherichia coli and Enterococci spp.) and zoonotic pathogens (E. coli O157: H7, Salmonella spp. and Campylobacter spp.) in water samples. In contrast, concentrations of conventional fecal indicator bacteria (FIB) were not correlated with zoonotic pathogens, suggesting that they are noneffective at detecting fecal pollution events. Collectively, the results obtained in this study demonstrated that a swine-targeted qPCR assay based on two Bacteroidales genes markers (gene 1-38, gene 3-53) could be a useful tool in determining the swine-associated impacts of fecal contamination in a watershed.

We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m). Through metagenomic analysis we found that microbial populations were mainly dominated by Bacteroidetes and Firmicutes. We identified 2210 common genes in the two groups. LEfSe showed that the distribution of Coprobacter, Geobacter, Cronobacter, Alloprevotella, and Dysgonomonas were more abundant in AF than AM. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing, environmental information processing, and cellular process were significantly enriched. Functional abundance was found to be associated with the nutrient absorption and microbial localization of indigenous chickens. We also investigated antibiotic resistant genes and found antibiotics like LSM, cephalosporin, and tetracycline were significantly more abundant in AF than AM.

Characterization of microbial communities inhabiting the reproductive tracts of cattle may lead to a better comprehension of bovine physiology and reproductive health. To date, reported studies have utilized culture-independent 16S ribosomal RNA (rRNA) for the classification of microbiota in the vaginal tract of cows but no studies have looked at the microbiota of the prepuce or penis of the bull. The aim of this study was to elucidate the microbiota present on the epithelial surface of the penis and prepuce of the post-pubertal bull using 16S rRNA gene sequencing. Ninety-two healthy bulls of a variety of ages and breeding history, presented for routine breeding soundness examinations, were utilized in this investigation. Bacteria belonging to Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria were identified in the prepuce. From all the bulls, two major community types were found, those with low or high bacterial species richness (up to 400 operational taxonomic units in one sample). There was no animal characteristic (breed or age) or management practice (feed type, antibiotic use, co-housing, breeding history) that was correlated with the bull penile microbial community composition. However, Bradyrhizobium was a distinguishing genus only found in the low diversity samples. The bull penile microbial community includes members of genera that are common in soil, cow vagina, respiratory tract, and feces. The baseline preputial microbial community in healthy bulls is described in the current study. This knowledge can be used later when investigating the interactions between disease and the male urogenital tract microbial community.

Consecutive replanting significantly affects the yield and quality of Atractylodes macrocephala due to replant disease. To explore the changes in the rhizosphere soil when atractylodes get replant disease, we detect soil physicochemical properties and the microbial community. The results show higher level of pH and phosphatase activity in the rhizo-soil of diseased plants than that of healthy ones. Moreover, 42 species of bacteria in the phylum of Acidobacteria, Gemmatimonadetes, Nitrospirae, Elusimicrobia, and Chlorobi show higher diversity, while 8 species in the phylum of Actinobacteria, Bacteroidetes, Firmicutes, and Fibrobacteres demonstrate lower diversity in that of diseased ones. In particular, decreased numbers of some beneficial bacteria including Sphingobium and Hyphomicrobium while increased numbers of pathogens such as Asticcacaulis, Rhizomicrobium in diseased ones may lead to replant disease. For fungi, there are 10 species with lower diversity in diseased ones, which belong to Ascomycota and Glomeromycota. In conclusion, microecological imbalance in Atractylodes rhizosphere caused by variation of the soil microbial community is considered the primary cause of replant disease. Some bacteria such as Sphingobium and some fungi including Alternaria alternate are closely related to the replant disease.

Inulin, a prebiotic, is an attractive alternative to antibiotic growth promoters in chickens. Dietary supplementation with inulin can improve growth performance, carcass yield, immune system activity, and serum biochemical parameters in chickens. A few studies investigated the impact of dietary inulin supplementation on chicken intestinal microbiota. In this study, we investigated how and why dietary supplementation with 1, 2, and 4% inulin can affect body weight gain, feed intake, food conversion rate, immunological parameters, serum biochemical parameters, and composition and dynamics of the cecal microbiota of Tegel broiler chickens using quantitative fluorescence in situ hybridization (qFISH). We showed that inulin inclusion has a negative effect on growth performance parameters before day 21 and a positive effect subsequently up to day 42. Quantitative FISH data revealed an age-dependent change in the cecal microbiota in the control broilers fed no inulin. Thus, relative abundances of Firmicutes and Actinobacteria decreased from 52.8 to 48.3% of total cells and from 8.7 to 1.4% at days 7 and 42, respectively. However, relative abundances of Bacteroidetes and Proteobacteria gradually increased from 9.3 to 26.9% of the total cells and from 10.7 to 21.1%, respectively, over the same periods. Inulin inclusion appeared to lower the relative abundances of Lactobacillus johnsonii and Bifidobacterium species at an early bird age, but it subsequently significantly (P < 0.05) increased their relative abundances. Such increases positively correlated with body weight gain of the birds, determined after day 21. Thus, dietary supplementation with inulin together with the addition of L. johnsonii and Bifidobacterium (B. gallinarum and B. pullorum) cultures at an early age may help overcome its early negative influence on growth performance. We believe that these findings can improve our knowledge on how inulin can change the intestinal microbiota of broiler chickens and help in developing an inulin feeding regime to optimize its beneficial role in chicken development.

Environmental enteric dysfunction (EED) is a subclinical condition of the gut characterized by changes in morphology and function with underlying chronic inflammatory responses. This study characterized composition and diversity of the gut microbiota in rural Malawian children with and without signs of EED. Fecal samples were collected from children aged 1–59 months. Neopterin, myeloperoxidase and alpha-1 antitrypsin concentrations were quantified by ELISA and combined to form a composite EED score using principal component analysis. DNA was extracted from fecal samples and V4-16S rRNA gene sequencing was used to characterize the gut microbiota. The concentrations of all three biomarkers decreased with increasing age, which is consistent with other studies of children living in similar low-income settings. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were the dominant phyla while Faecalibacterium and Bifidobacterium were the most prevalent genera. Increased alpha diversity was associated with a reduction in neopterin concentration. Microbiota composition was different between fecal samples with low and high composite EED scores; increased abundance of Succinivibrio was associated with reduced composite EED scores., Highlights • Fecal concentrations of myeloperoxidase, alpha-1 antitrypsin and neopterin decreased with age in Malawian children. • A marginal negative association was found between alpha diversity of the gut microbiota and fecal neopterin concentration. • Succinivibrio abundance was higher in children with reduced composite environmental enteric dysfunction biomarker score. • Modelling found 3 metagenomic-metabolic pathways associated with a reduced risk of high composite biomarker score., Gut microbiota; V4-16S rRNA sequencing; PICRUSt2; Environmental enteric dysfunction.

In this work, the influence of different forms of presentation of chitosan in the human gut microbiota with a defined bacterial community was evaluated. First, the susceptibility of individual gut bacterial isolates against chitosan was studied within a concentration range between 0.125 and 1 mg/mL. Then, the impact of chitosan (0.25 and 1 mg/mL) on a defined human gut microbial ecosystem was studied by metagenomic and metabonomic analyses. The results showed that chitosan in its free form had a high impact on individual isolates with a minimum inhibitory concentration below 1 mg/mL for most of the strains studied. In comparison, chitosan immobilized in the different carriers displayed a diverse effect on gut microbiota. The most susceptible strains were Agathobacter rectalis strain 16-6-I 1 FAA, Clostridium spiroforme strain 16-6-I 21 FAA and Mediterraneibacter faecis strain 16-6-I 30 FAA. The impact of the different modes of presentation of chitosan was strain-specific and species-specific when compared to results obtained from analysis of other strains within the genera Agathobacter, Clostridium and Mediterraneibacter, and therefore a study using a defined ecosystem was needed to extrapolate the results. Significant decreases in defined community richness and diversity and changes in metabolic profile were observed after exposure to free chitosan. Free chitosan produced significant reductions in the abundance of the genera Lachnoclostridium, Anaerotignum, Blautia, Enterococcus, Eubacterium and Ruthenibacterium together with a slight decrease of the production of SCFAs, among other fermentation by-products. The immobilized chitosan significantly alleviated the impact caused by the antimicrobial polymer and significantly increased the relative abundance of the Bacteroidetes phylum compared to free chitosan. These results suggest the significance of assessing the impact of new ingredients and materials included in food on the human gut microbiota with models that simulate the gastrointestinal environment, such as in vitro bioreactor systems.

Fish-related antibiotic resistance genes (ARGs) have attracted attention for their potentially harmful effects on food safety and human health through the food chain transfer. However, the potential factors affecting these ARGs have not been fully explored. In this study, ARGs and bacterial communities in the fish gut, mucosal skin, and gill filaments in fish were comprehensively evaluated in four different mariculture systems formed by hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), Gracilaria bailinae, and Litopenaeus vannamei using different combinations. The results showed that 9 ARGs were detected in the gut and mucosal skin and 6 ARGs in the gill filaments. The detection rate of aphA1 was the highest, and the abundance was 1.91 × 10

The impact of scleral protein shell (SPS) amendment on bacterial community succession during pig manure (PM) composting were evaluated in the present work. Five treatments representing different dry weight dosage of SPS [0 % (T1), 2.5 % (T2), 5 % (T3), 7.5 % (T4), 10 % (T5) and 12 % (T6)] were applied with initial mixture of raw materials (Wheat straw along with the PM) and composted for 42 days. Results indicated that the dominant of phyla were Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. The relative abundance (RA) of genus un-identified, Ruminofilibacter, Thermovum, Longispora and Pseudomonas were greater among the all treatments but interestingly genus Ruminofilibacter was also higher in control treatment. The network analysis was confirmed that T6 treatment with higher dosage of SPS amendment could enhance the bacterial population and rate of organic matter mineralization. Compared with T1, the T5 has greater potential impact to enhance the bacterial population and significant correlation among the pH and temperature.

This study investigated the structure of fungal and bacterial communities in different types of Cd-contaminated soils. The results showed that obvious variations in microbial structure between contaminated alkaline soils and acidic soils. Proteobacteria, Gemmatimonadetes, Bacteroidetes and Basidiomycota dominated the studied communities in the alkaline soils, whereas Actinobacteria, Chloroflexi, Firmicutes, Acidobacteria, Saccharibacteria and Ascomycota were more abundant in the acidic soils. Additionally, Cd tolerant (Proteobacteria, Bacteroidetes, Ascomycota) and sensitive (Actinobacteria, Acidobacteria, Basidiomycota) in alkaline soils and JL-soils, Cd tolerant (Actinobacteria, Acidobacteria, Basidiomycota) and sensitive (Saccharibacteria, Proteobacteria, Bacteroidetes, Ascomycota, Mucoromycota) in the acidic soils were identified. Redundancy analysis and correlation analysis demonstrated that it was significantly affected by different environment parameters in alkaline soils and acidic soils. Varied bacterial community structures in all soils were dominantly influenced by pH and SOM. The similarities among different groups indicated the effect of soil type on microbial community structure was greater than that of Cd level. The above conclusions may provide a new perspective for the bio-remediation of Cd in different types of soils.

Mitochondrial DNA (mtDNA) is used as a genetic marker to track fecal contamination in surface water. Its potential to effectively discriminate between the nonpoint sources of fecal pollution (e.g. human, livestock) in water environments is relevant for water quality management. However, there is a lack of knowledge about the environmental persistence of mtDNA in relation to those of other microbial parameters, such as fecal indicator bacteria (FIB). In this study, mesocosms composed of water collected from four rivers and tap water were spiked with raw wastewater to mimic human fecal contamination. Mesocosms composed of raw wastewater were also studied. The mesocosms were incubated at 4 °C or at 22 °C for 189 days, from which the levels of human mtDNA (HumtDNA) and human Bacteroidales (Hf183) were measured by qPCR. The levels of FIB (fecal coliforms and enterococci) and heterotrophs were determined by culture methods along with the determination of physicochemical attributes. The decay rates of the genetic markers and FIB were determined with first-order decay rate models. The decay rates of HumtDNA (0.004-0.059 d

Antibiotic-induced gut dysbiosis is believed to be associated with the onset and development of autoimmune diseases. To evaluate microbiota's variations triggered by antibiotic therapy and its outcomes on autoimmune diseases, preclinical studies regarding these subjects were included in this review. The studies were selected on PubMed, Scopus and Web of Science from 2011 to 2021 by three researchers that extracted study data and risk of bias, which were verified by a further 3 independent researchers. The team assessed the strength of evidence across studies. Of the eligible studies, 17 showed an improvement of the studied disease after antibiotic therapy and 10 had a negative effect on the course of the condition. The ameliorating factors of the studied diseases were mostly seen when using an antibiotic cocktail. Male animals had a good outcome after therapy and, for all genders, the increase in IL-10 and Treg cells was often shown to ameliorate disease after the antibiotic intervention. Firmicutes, Proteobacteria and Bacteroidetes appeared altered after the antibiotic intervention, leading to amelioration or worsening of the condition depending on the autoimmune disease. We identified that the number of autoimmune conditions approached leads to specific conclusions regarding the interventions, making it difficult to achieve an overall conclusion. Overall, even though pre-clinical studies must be translated to the human model, the studied aspects of gender, age, lineage and disease model substantially impact the outcomes that make for many intricacies that were not-established in the study of antibiotic-induced gut dysbiosis and autoimmunity.

Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.

Astragalus polysaccharide (APS) plays important roles in antibacterial, antiviral and antiparasitic activities in mammals, birds and aquatic animals. However, the relationship between non-specific immune responses and intestinal microbiota in sea cucumber (Apostichopus japonicus) after dietary APS supplementation has not been reported to date. Here, the effect of dietary APS supplementation on the non-specific immune response and intestinal microbial composition and species distribution of sea cucumber was explored. We found that although there was no significant effect on sea cucumber growth, the enzymatic activity and expression level of immune- and antioxidant-related genes changed after dietary APS supplementation. Furthermore, the intestinal microbial composition and species distribution of sea cucumber were different at the phylum and genus levels after dietary APS supplementation. The phyla Proteobacteria and Bacteroidetes were significantly different between the APS2 group and CK group. The results of PCA and PCoA analysis also showed that the APS2 group was significantly different compared to the other groups. Finally, analysis of the relationship between non-specific immune responses and the intestinal microbiota showed that the expression level of NF-κB was significantly correlated with intestinal microbiota at the genus level. This finding suggests that dietary APS supplementation might affect the non-specific immune response and intestinal microbiota of sea cucumber through the NF-κB signalling pathway; the appropriate added level was 800 mg/kg. Taken together, our results lay a foundation for further understanding the relationship between non-specific immune responses and intestinal microbial of sea cucumber.

Municipal sludge compost contains residual heavy metals (HMs), which could limit the utilization of compost as a resource. Studies have revealed that the availabilities of HMs in composting system are affected by microbial-driven organic matter and physicochemical indices. However, how the microbial community dynamics affect the availability of HMs during municipal sludge composting remains unclear. In this study, high-throughput sequencing technology was applied to investigate the response relationship between microbial dynamics and different availability of HMs. A total of 31 main genera within 5 phyla were identified. The concentrations of the most available HMs increased, and the increasing rates varied from 102% to 240%. Proteobacteria, Firmicutes, and Chloroflexi could affect organic matter to control the phytoavailability of Cr and Pb, whereas Proteobacteria, Bacteroidetes, and Actinobacteria could affect the phytoavailability of Cu and Zn. The bioaccessible HMs are only affected by organic functional groups, whereas the leachable HMs are not affected by organic matter or microorganisms. The “physicochemical index-microorganisms-available heavy metal” response pathway and principal component analysis showed that the increase in total C and N and the decreasing content of NO3−–N reduce the phytoavailable HMs. We finally proposed a regulation method to improve the resource utilization of municipal sludge composting and provide theoretical support for the harmlessness of municipal sludge composting.

Fatty liver is widely observed during Takifugu fasciatus production, but the mechanisms underlying fatty liver formation remain unknown. The present study was conducted to determine the potential effects of copper (Cu) on hepatic lipid deposition and metabolism in T. fasciatus after 21 days of exposure to Cu (levels: 0, 20 and 100 μg/L). Copper exposure decreased the weight gain rate (WG) in T. fasciatus, but increased the values of the viscerosomatic index (VSI) and hepatosomatic index (HSI) compared with the control. The time-dependent Cu accumulation in tissues increased as the Cu concentration increased. The order of Cu accumulation was liver > intestine > muscle. The lipid content, triglyceride (TG) content and lipoprotein lipase (LPL) activity increased after Cu exposure compared with the control. In addition, more lipid droplets and greater vacuolization were observed in the liver after exposure to 20 μg/L Cu than after 100 μg/L Cu. The expression of genes involved in lipogenesis (g6pd, 6pgd, lpl, fas and acc), lipolysis (hsl and cpt 1) and transcription (ppar α and ppar ©) was dependent on Cu. An analysis of the intestinal microbiome community showed that the highest values of the Chao 1 index, ACE, Shannon index and Simpson index were obtained in fish exposed to 20 μg/L Cu, whereas the lowest values were obtained after the 100 μg/L Cu treatment. The Principal Coordinates Analysis (PCoA) plots of the data revealed structural differences in the groups treated with Cu compared with the control group. At the phylum level, the intestinal microbiota in the Cu-treated and control fish were dominated by Proteobacteria and Bacteroidetes. The higher Firmicutes to Bacteroidetes ratio was observed in fish treated with 20 μg/L Cu compared with other groups, while the lowest ratio was observed in fish exposed to 100 μg/L Cu. Our study revealed the mechanisms by which Cu exposure altered (i) lipid deposition in the body and (ii) the intestinal microbiome, which may contribute to maintain the health status of T. fasciatus for the aquaculture.

In this study, nitrogen transformation strains, including three ammonium transformation strains, one nitrite strain and one nitrogen fixer, were inoculated at different swine carcass composting stages to regulate the nitrogen transformation and control the nitrogen loss. The final total nitrogen content was significantly increased (p 0.01). The bacterial communities were assessed by amplicon sequencing and association analysis. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were the four most dominant phyla.,Brevibacterium, Streptomyces and Ochrobactrum had a significant (p 0.05) and positive correlation with total nitrogen and ammonium nitrogen content in both groups. The quantitative results of nitrogen transformation genes showed that ammonification, nitrification, denitrification and nitrogen fixation were simultaneously present in the composting process of swine carcasses, with the latter two accounting for a higher proportion. The ammonium transformation strains significantly (p 0.05) strengthened nitrogen fixation and remarkably (p 0.01) weakened nitrification and denitrification, which, however, were notably (p 0.05) enhanced by the nitrite strain and nitrogen fixer. In this research, the inoculated strains changed the bacterial structure by regulating the abundance and activity of the highly connected taxa, which facilitated the growth of nitrogen transformation bacteria and regulated the balance/symbiosis of nitrogen transformation processes to accelerate the accumulation of nitrogen.

Background Obesity is a leading contributor to numerous diseases, such as diabetes mellitus, cardiovascular diseases, and cancers. Therefore, seeking effective and safe approaches to control obesity is essential. Gut microbiota has been demonstrated to play a critical role in the occurrence of obesity via the regulation of energy metabolism. The composition and abundance of gut microbiota can be altered by the diet. Recently, many dietary plants have been demonstrated to exert anti-obesity effects through bioactive components that modulate gut microbiota, which has drawn increasing research attention. Scope and approach In this review, the obesity-associated gut microbiota has been summarized and classified into obesogenic and anti-obesity categories. Subsequently, some anti-obesity dietary plants with gut microbiota-modulating activities and the mechanisms of action of their bioactive components are discussed. Key findings and conclusions The effects of gut microbiota on obesity have been found in most animal and some human studies. Certain strains of Firmicutes, Lactobacillus, and Bacteroidetes are positively associated with obesity development, while Bifidobacterium, most Lactobacillus, and some Bacteroidetes show anti-obesity activities. Some dietary plants, such as grapes, berries, apple, turmeric, chili, soy, sorghum, and barley, show anti-obesity efficacy through increasing the diversity of gut microbiota, up-regulating anti-obesity gut microbiota and down-regulating obesogenic gut microbiota. This review may stimulate further development of functional foods to treat obesity through modulating gut microbiota. Future work will rely on the exploration of more dietary plants and their components with anti-obesity and gut microbiota-modulating effects, and further investigation of related mechanisms as well as clinical trials.