Genus Prevotella Research Articles

The gut microbiome is associated with markers of cerebral small vessel disease

AbstractBackgroundCerebral small vessel disease (cSVD) is a major cause of cognitive impairment and dementia in the elderly. Dysregulation of the gut microbiome has been linked to cSVD, stroke, and dementia in human and animal studies. However, whether dysbiosis is associated with markers of cSVD is unclear. We aimed to assess the cross‐sectional association between the gut microbiome and MRI markers of cSVD and executive function in the Framingham Heart Study (FHS).MethodWe included FHS participants from the Third‐generation cohort without a history of stroke or dementia. We estimated the gut microbiota composition using 16S rRNA gene sequencing. MRI markers of cSVD included white matter hyperintensities (WMH) and peak width of skeletonized mean diffusivity (PSMD). Executive function was assessed as the difference between the Trail Making Test (TMT) part B and A. We used multivariable regression analysis to evaluate the association between the gut microbiota and WMH, PSMD, and TMT, adjusting for age, age2, sex, BMI, and education. Additionally, we used differential abundance analysis to explore extremes of cSVD markers dichotomized by their distribution with the upper quintile representing the least healthy group. Finally, we used PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to gain insight into the functional profiles of the underlying microbial communities.ResultOur sample included 972 participants (age: 55 ± 10 years, 56% female). Using multivariable models, we found that greater abundance of genera Pseudobutyrivibrio and Ruminococcus were associated with lower (healthier) WMH and PSMD (p‐values < 0.001), as well as better executive function (p‐values < 0.01). Furthermore, the differential analysis indicated a lower abundance of the genus Prevotella in the group of participants with the highest (least healthy) PSMD and WHM (p‐values < 0.05). Finally, functional analyses using PICRUSt implicated various KEGG pathways, including carbohydrate metabolism, glycosaminoglycan, and fatty acid biosynthesis previously associated with cognitive performance.ConclusionOur study suggests abundance of certain gut bacteria in genus Pseudobutyrivibrio, Ruminococcus, and Prevotella, that produce butyric acid and other metabolites used by the human brain, are associated with healthier brain vasculature and better cognitive function in middle‐aged healthy adults.

Effects of dietary supplementation with a blend of functional oils to fecal microbiota, and inflammatory and oxidative responses, of dogs submitted to a periodontal surgical challenge

We aimed to evaluate the effects of functional oils from copaiba (Copaifera spp.), cashew nut shell (Anacardium occidentale), and pepper species (Schinus molle L. and Capsicum annum L.) on coefficients of total tract apparent digestibility (CTTAD) of nutrients, intestinal fermentative metabolites, fecal microbiota, and inflammatory and oxidative markers in dogs submitted to periodontal surgery. Two treatments were evaluated: control and test, containing the blend of functional oils (0.1 g/animal/day). The oil blend contained 280 g/kg cashew nut shell (Anacardium ocidentalle) oil, 60 g/kg Capsicum annuum L. and Schinus molle L. pepper species oils, and 60 g/kg copaiba (Copaifera spp.) oil. The treatments were offered for 35 days to 12 adult Beagle dogs, distributed in a completely randomized design (n = 6). On day 30, the dogs were submitted to periodontal surgery. Fecal (days 30 and 35) and blood (days 0, 30, and 35) samples were collected for the evaluation of intestinal fermentative metabolites, fecal microbiota, and inflammatory and antioxidant responses in the blood. Dogs of the control group presented a more pronounced reduction in the genera Prevotella and Faecalibacterium after surgery (day 35) than the test group (P < 0.05). Besides, dogs of the control group also presented a greater abundance of Streptococcus on day 35 (P < 0.05). There was an increase in NF-κB concentration in the blood after surgery only in the control group (P < 0.05). Additionally, dogs fed the oil blend showed lower lipid peroxidation (P < 0.05) and a tendency (P = 0.059) to higher glutathione transferase activity. The blend of functional oils does not alter the digestibility of nutrients and may modulate the intestinal microbiota. Furthermore, it controls the inflammatory and oxidative mechanisms after the surgical challenge in dogs.

Enterotypical Prevotella and three novel bacterial biomarkers in preoperative stool predict the clinical outcome of colorectal cancer

BackgroundA significant proportion of colorectal cancer (CRC) patients suffer from early recurrence and progression after surgical treatment. Although the gut microbiota is considered as a key player in the initiation and progression of CRC, most prospective studies have been focused on a particular pathobionts such as Fusobacterium nucleatum. Here, we aimed to identify novel prognostic bacteria for CRC by examining the preoperative gut microbiota through 16S ribosomal RNA gene sequencing.ResultsWe collected stool samples from 333 patients with primary CRC within 2 weeks before surgery and followed up the patients for a median of 27.6 months for progression and 43.6 months for survival. The sequence and prognosis data were assessed using the log-rank test and multivariate Cox proportional hazard analysis. The gut microbiota was associated with the clinical outcomes of CRC patients (Pprogress = 0.011, Pdecease = 0.007). In particular, the high abundance of Prevotella, a representative genus of human enterotypes, indicated lower risks of CRC progression (P = 0.026) and decease (P = 0.0056), while the occurrence of Alistipes assigned to Bacteroides sp., Pyramidobacter piscolens, Dialister invisus, and Fusobacterium nucleatum indicated a high risk of progression. A microbiota-derived hazard score considering the five prognostic bacteria accurately predicted CRC progression in 1000 random subsamples; it outperformed widely accepted clinical biomarkers such as carcinoembryonic antigen and lymphatic invasion, after adjustment for the clinicopathological stage (adjusted HR 2.07 [95% CI, 1.61–2.64], P = 7.8e−9, C-index = 0.78). PICRUSt2 suggested that microbial pathways pertaining to thiamine salvage and L-histidine degradation underlie the different prognoses.ConclusionsThe enterotypical genus Prevotella was demonstrated to be useful in improving CRC prognosis, and combined with the four pathobionts, our hazard score based on the gut microbiota should provide an important asset in predicting medical outcomes for CRC patients.48KLrU1kw-NevPNeR-hyqwVideo

Effect of Entamoeba histolytica infection on gut microbial diversity and composition in diarrheal patients from New Delhi.

During amoebiasis, colonization of the gut by Entamoeba histolytica can lead to alterations of the host microbiota. In this study, we have compared the gut microbiota of patients of amoebiasis with healthy controls using 16S rRNA gene variable regions, (V1-V3) and (V3-V5), of the bacterial genome. From this 16S rRNA gene amplicon data, one paired-end and two single-end datasets were selected and compared by the number of OTUs obtained, sequence count, and diversity analysis. Our results showed that the V1-V3-paired-end dataset gave the maximum number of OTUs in comparison to the two single-end datasets studied. The amoebiasis samples showed a significant drop in richness in the alpha diversity measurements and lower intra group similarity compared to the healthy controls. Bacteria of genus Prevotella, Sutterella, and Collinsella were more abundant in healthy controls whereas Escherichia, Klebsiella, and Ruminococcus were more abundant in the E. histolytica-positive patients. All the healthy controls harbored bacteria belonging to Faecalibacterium, Prevotella, Ruminococcus, Subdoligranulum, and Escherichia genera while all the E. histolytica-positive patient samples contained genus Enterobacter. The compositional changes in the gut microbiome observed in our study indicated a higher prevalence of pathogenic bacteria along with a depletion of beneficial bacteria in E. histolytica-infected individuals when compared with healthy controls. These results underline the interplay between E. histolytica and the human gut microbiome, giving important inputs for future studies and treatments.

Microbiota of vaccinated and non-vaccinated clinically inconspicuous and conspicuous piglets under natural Lawsonia intracellularis infection.

Lawsonia (L.) intracellularis is a widespread, economically important bacterium causing the porcine proliferative enteropathy (PPE). In this study, we evaluated intestinal microbiota of naturally exposed L. intracellularis-positive pigs under standardized conditions. To obtain three independent repetitions, 27 L. intracellularis-infected pigs (19.0 ± 1.50 kg body weight) from one farm were divided into three groups at an age of 7 to 8 weeks (nine pigs/group). Pigs were either vaccinated against L. intracellularis via oral drenching on their 21st day of life (attenuated live vaccine) or non-vaccinated and selected according to clinical findings (pigs without deviating fecal consistency or with moderate to soft fecal consistency). Comparison of the clinically inconspicuous piglets that differed regarding their vaccination status showed fewer significant differences in fecal microbiota composition. The vaccination led to an overall enrichment of bacterial species belonging to the order Clostridiales, while species of the genus Collinsella and Prevotella were decreased. Several bacterial species belonging to the order Bacteroidales, mainly of the family Prevotellacecae, often closely matching Prevotella copri differed significantly between non-vaccinated clinically inconspicuous and conspicuous piglets. Whether those bacterial species play a role in mitigating the severity of an L. intracellularis infection remains to be defined.

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing.

To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a higher abundance of Prevotella genus than DHB and YS pigs. The functional profiles varied among the three pig breeds, DNSE pigs had more active carbohydrate metabolism and more abundant antibiotic resistance genes than the other two pig breeds. Moreover, we found that peptide and macrolide resistances genes in DNSE pigs were more abundant than that in DHB pigs (p < 0.05). This study will help to provide a theoretical basis for the development of native pig breeds in Yunnan Province, China.

Dietary Stevia Residue Extract Supplementation Improves Antioxidant Capacity and Intestinal Microbial Composition of Weaned Piglets.

This study aimed to investigate the effects of diet supplementation with stevia residue extract (SRE) on growth performance, intestinal health, and antioxidant capacity of weaned piglets. A total of 144 weaned piglets (body weight 6.8 ± 0.5 kg) were randomly selected and allocated into four treatment groups with six replicates of six pigs/pen. The treatments consisted of a basal diet without SRE or basal diet supplemented with 100, 200, or 400 mg/kg SRE. The results showed that the addition of 200 mg/kg SRE to the diet significantly reduced (p < 0.05) the diarrhea rate of piglets compared with the control group. The supplementation of 400 mg/kg SRE in the diet significantly reduced the piglets’ serum MDA content and significantly increased (p < 0.05) the T-AOC, T-SOD, and GSH-PX activity in the serum. The dietary supplementation with 400 mg/kg SRE significantly increased (p < 0.05) the CAT and GSH-PX activity in the liver. Moreover, the supplementation of 400 mg/kg SRE in the diet significantly increased (p < 0.05) the relative abundance of Prevotellaceae (genus) and Roseburia (genus) beneficial bacteria compared to the control group. Spearman’s correlation analysis showed that Prevotella (genus) abundance was positively correlated with liver GSH-PX activity and acetic acid content of colon contents. In conclusion, the supplementation of 400 mg/kg SRE to the diet can improve piglet health by regulating antioxidant reduction homeostasis, which may also be associated with an increase in the relative numbers of potentially beneficial bacteria.

The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that fall into two main categories: Crohn’s disease (CD) and ulcerative colitis (UC). The gastrointestinal tract extends from the mouth to the anus and harbors diverse bacterial communities. Several sequencing-based studies have identified an intestinal enrichment of oral-associated bacteria and demonstrated their ability to induce intestinal inflammation in mice, suggesting that intestinal pathobionts originate from the oral cavity, particularly members of the genus Streptococcus. This study aimed to investigate the composition of the salivary and fecal microbiome of IBD patients (n = 14) compared to healthy controls (n = 12) and to determine the abundance of common bacterial taxa in both niches. Metagenomic DNA was extracted from saliva and fecal samples, and the 16S rRNA gene was targeted for sequencing. Our results revealed that the overall microbial composition of saliva was significantly altered in the IBD patients compared to the control subjects (p = 0.038). At the genus level, Veillonella and Prevotella were highly abundant in IBD (median: 25.4% and 22.2%, respectively) compared to the control group (17.9% and 13.4%, respectively). In contrast, Neisseria, Streptococcus, Haemophilus, and Fusobacterium were associated with a healthy gut state. Regarding the fecal microbiome, the IBD group had a significantly higher abundance of Clostridium sensu stricto 1 and Escherichia-Shigella (both comprising pathogenic bacteria) compared with the control group. Members of both bacterial groups have previously been shown to positively correlate with intestinal inflammation and high expression of pro-inflammatory cytokines that disrupt intestinal barrier integrity. In addition, we demonstrate that the increased abundance of Clostridium sensu stricto 1 and Escherichia-Shigella has also been associated with significant upregulation of certain metabolic pathways in the feces of the IBD group, including bacterial invasion of epithelial cells. Streptococcus was the only common genus detected in both the salivary and fecal microbiome and represented the oral-gut axis in our study. Using culture-based methods, we isolated 57 and 91 Streptococcus strains from saliva as well as 40 and 31 strains from fecal samples of the controls and IBD patients, respectively. The phylogenetic tree of streptococci based on sodA sequences revealed several patient-specific clusters comprising salivary and fecal streptococcal isolates from the same patient and belonging to the same species, suggesting that the oral cavity is an endogenous reservoir for intestinal strains.

The impact of short-chain fatty acid-producing bacteria of the gut microbiota in hyperuricemia and gout diagnosis.

Persistent hyperuricemia is a key factor in gout; however, only 13.5% of hyperuricemic individuals manifest the disease. The gut microbiota could be one of the many factors underlying this phenomenon. We aimed to assess the difference in taxonomic and predicted functional profiles of the gut microbiota between asymptomatic hyperuricemia (AH) individuals and gout patients. The V3-V4 region of the 16S rRNA gene of the gut microbiota of AH individuals, gout patients, and controls was sequenced. Bioinformatic analyses were carried out with QIIME2 and phyloseq to determine the difference in the relative abundance of bacterial genera among the study groups. Tax4fun2 was used to predict the functional profile of the gut microbiota. AH individuals presented a higher abundance of butyrate- and propionate-producing bacteria than gout patients; however, the latter had more bacteria capable of producing acetate. The abundance of Prevotella genus bacteria was not significantly different between the patients but was higher than that in controls. This result was corroborated by the functional profile, in which AH individuals had less pyruvate oxidase abundance than gout patients and less abundance of an enzyme that regulates glutamate synthetase activation than controls. We observed a distinctive taxonomic profile in AH individuals characterized by a higher abundance of short-chain fatty acid-producing bacteria in comparison to those observed in gout patients. Furthermore, we provide scientific evidence that indicates that the gut microbiota of AH individuals could provide anti-inflammatory mediators, which prevent the appearance of gout flares. Key Points • AH and gout patients both have a higher abundance of Prevotella genus bacteria than controls. • AH individuals' gut microbiota had more butyrate- and propionate-producing bacteria than gout patients. • The gut microbiome of AH individuals provides anti-inflammatory mediators that could prevent gout flares.

Elucidation of the initial bacterial community of Ezine PDO cheese using next-generation sequencing.

This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47-56.07%, 7.33-20.34%, and 1.21-25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24-54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50-23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.

The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults

Advancing age coincides with changes in the gut microbiome and a decline in cognitive ability. Psychobiotics are microbiota-targeted interventions that can result in mental health benefits and protect the aging brain. This study investigated the gut microbiome composition and predicted microbial functional pathways of middle-aged and older adults that met criteria for mild cognitive impairment (MCI), compared to neurologically healthy individuals, and investigated the impact of probiotic Lactobacillus rhamnosus GG (LGG) in a double-blind, placebo-controlled, randomized clinical trial. A total of 169 community-dwelling middle-aged (52-59 years) and older adults (60-75 years) received a three-month intervention and were randomized to probiotic and placebo groups. Participants were further subdivided based on cognitive status into groups with intact or impaired cognition and samples were collected at baseline and post supplementation. Microbiome analysis identified Prevotella ruminicola, Bacteroides thetaiotaomicron, and Bacteroides xylanisolvens as taxa correlated with MCI. Differential abundance analysis at baseline identified Prevotella as significantly more prevalent in MCI subjects compared to cognitively intact subjects (ALDEx2 P =0.0017, ANCOM-BC P =0.0004). A decrease in the relative abundance of the genus Prevotella and Dehalobacterium in response to LGG supplementation in the MCI group was correlated with an improved cognitive score. Our study points to specific members of the gut microbiota correlated with cognitive performance in middle-aged and older adults. Should findings be replicated, these taxa could be used as key early indicators of MCI and manipulated by probiotics, prebiotics, and symbiotics to promote successful cognitive aging. Registered under ClinicalTrials.gov Identifier no. NCT03080818.

Composition of the Gut Microbiota Associated with the Response to Immunotherapy in Advanced Cancer Patients: A Chinese Real-World Pilot Study.

Background: The composition of the gut microbiota is associated with the response to immunotherapy for different cancers. However, the majority of previous studies have focused on a single cancer and a single immune checkpoint inhibitor. Here, we investigated the relationship between the gut microbiota and the clinical response to anti-programmed cell death protein 1 (PD-1) immunotherapy in patients with advanced cancers. Method: In this comprehensive study, 16S rRNA sequencing was performed on the gut microbiota of pre-immunotherapy and post-immunotherapy, of 72 advanced cancer patients in China. Results: At the phylum level, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the main components of the microbiota in the 72 advanced cancer patients. At the genus level, Bacteroides and Prevotella were the dominant microbiota among these 72 patients. The PD_whole_tree, Chao1, Observed_species and Shannon indices of R.0 and R.T were higher than those of NR.0 and NR.T. The results of LEfSe showed that Archaea, Lentisphaerae, Victivallaceae, Victivallales, Lentisphaeria, Methanobacteriaceae, Methanobacteria, Euryarchaeota, Methanobrevibacter, and Methanobacteriales were significantly enriched in the response group before immunotherapy (R.0), and the Clostridiaceae was significantly enriched in the non-response group before immunotherapy (NR.0) (p < 0.05). Lachnospiraceae and Thermus were significantly enriched in the response group after immunotherapy (R.T), and Leuconostoc was significantly enriched in R.0 (p < 0.05). ROC analysis showed that the microbiota of R.T (AUC = 0.70) had obvious diagnostic value in differentiating Chinese cancer patients based on their response to immunotherapy. Conclusions: We demonstrated that the gut microbiota was associated with the clinical response to anti-PD-1 immunotherapy in cancer patients. Taxonomic signatures enriched in responders were effective biomarkers to predict the clinical response. Our findings provide a new strategy to improve the efficiency of responses to immunotherapy among cancer patients.

Tannic acid reduced apparent protein digestibility and induced oxidative stress and inflammatory response without altering growth performance and ruminal microbiota diversity of Xiangdong black goats.

The present study was performed to evaluate the impacts of tannic acid (TA) supplementation at different levels on the growth performance, physiological, oxidative and immunological metrics, and ruminal microflora of Xiangdong black goats. Twenty-four goats were randomly assigned to four dietary treatments: the control (CON, basal diet), the low-dose TA group [TAL, 0.3 % of dry matter (DM)], the mid-dose TA group (TAM, 0.6 % of DM), and the high-dose TA group (TAH, 0.9 % of DM). Results showed that the growth performance was unaffected (P > 0.05) by adding TA, whilst the 0.3 % and 0.6 % TA supplementation significantly decreased (P < 0.05) the apparent digestibility of crude protein (CP) and ruminal NH3-N concentration, and raised (P < 0.05) the level of total volatile fatty acid (TVFA) in rumen. The increments of alanine aminotransferase (ALT), triglyceride (TG), cortisol (CORT), total antioxidant capacity (T-AOC), interleukin (IL)-1β, IL-6, and serumamyloid A (SAA), and decrements of globulin (GLB), immunoglobulin G (IgG), cholinesterase (CHE), glutathione reductase (GR), creatinine (CRE), growth hormone (GH), high-density lipoprotein cholesterol (HDLC), and insulin-like growth factor 1 (IGF-1) to different extents by TA addition were observed. Although the Alpha and Beta diversity of rumen bacterial community remained unchanged by supplementing TA, the relative abundance of the predominant genus Prevotella_1 was significantly enriched (P < 0.05) in TAL. It could hence be concluded that the TA supplementation in the present trial generally decreased CP digestion and caused oxidative stress and inflammatory response without influencing growth performance and ruminal microbiota diversity. More research is needed to explore the premium dosage and mechanisms of effects for TA addition in the diet of goats.

Age-dependent variations in rumen bacterial community of Mongolian cattle from weaning to adulthood

BackgroundRumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that the rumen microbiome of Mongolian cattle has adapted to degrade the rough forage to provide sufficient energy to tolerate the harsh desert ecological conditions. However, little is known about the succession of rumen microbes in different developmental stages of post-weaning Mongolian cattle.MethodsHere, we examined the succession of the rumen microbial composition and structure of 15 post-weaning Mongolian cattle at three developmental stages i.e., 5 months (RM05), 18 months (RM18) and, 36 months (RM36) by using the 16S rRNA gene sequencing method.ResultsWe did not find any age-dependent variations in the ruminal concentrations of any volatile fatty acid (VFA) of Mongolian cattle. The diversity of the rumen bacterial community was significantly lower in RM05 group, which reached to stability with age. Bacteroidetes and Firmicutes were the two dominant phyla among all age groups. Phylum Actinobacteria was significantly higher in RM05 group, phyla Spirochaetes, and Tenericutes were highly abundant in RM18 group, and phyla Proteobacteria and Epsilonbacteraeota were enriched in RM36 group. Genera Prevotella_1, Bacteroides, and Bifidobacterium were abundant in RM05 group. The short chain fatty acid (SCFA) producing bacteria Rikenellaceae_RC9_gut_group showed high abundance in RM18 group and fiber degrading genus Alloprevotella was highly abundant in RM36 group. Random forest analysis identified Alloprevotella, Ileibacterium, and Helicobacter as important age discriminatory genera. In particular, the genera Ruminococcaceae_UCG-005, Bacteroides, Saccharofermentans, and Fibrobacter in RM05, genera [Eubacterium] coprostanoligenes_group, Erysipelotrichaceae_UCG-004, Helicobacter, Saccharofermentans, Papillibacter, and Turicibacter in RM18, and genera Rikenellaceae_RC9_gut_group, Lachnospiraceae_AC2044_group, and Papillibacter in RM36 showed the top interactions values in the intra-group interaction network.ConclusionsThe results showed that rumen microbiota of Mongolian cattle reached to stability and maturity with age after weaning. This study provides some theoretical evidence about the importance of functional specific rumen bacteria in different age groups. Further studies are needed to determine their actual roles and interactions with the host.

Preliminary Investigation of the Effects of Rosemary Extract Supplementation on Milk Production and Rumen Fermentation in High-Producing Dairy Cows.

Rosemary extract (RE) has been used as an antioxidant in cosmetics and food additives, indicating its potential as a feed additive to improve adaptation in high-producing dairy cows. Here, we investigated the effects of RE supplementation on lactation performance and rumen fermentation in high-producing dairy cows. Thirty multiparous cows were blocked into 15 groups based on milk production and were randomly assigned to one of two treatments: 0 or 28 g/d of RE supplementation to the basic diet per cow. The experiment was conducted over a 74-day period, which included an initial two-week adaptation period. We observed significant increases in milk and milk lactose yields following RE supplementation. Somatic cell count tended to decrease by treatment. Additionally, superoxide dismutase concentration significantly increased and malonaldehyde level decreased after RE supplementation. Sequencing of 16S rRNA revealed that RE supplementation significantly affected the microbial composition and decreased the richness of the microbiota. Specifically, the abundance of the genus Prevotella was significantly decreased by RE supplementation and was correlated with volatile fatty acids in the Mantel test, whereas no significant correlation was found for other genera. Our findings provide fundamental information on the potential for RE as a feed additive for dairy cows to improve antioxidant status and enhance propionate generation.

The Potential Use of Endophyte-Free inebrians as Sheep Feed Evaluated with In Vitro Fermentation

Endophytic fungal infection is the major reason for intoxication of animals caused by drunken horse grass. Fortunately, it has been established that seed detoxification techniques and isolation of endophytic fungi infect non-endophytic fungi populations with the same genetic background as endophyte-infected Achnatherum inebrians. Moreover, sheep can use endophyte-free Achnatherum inebriants (EF) without obvious toxicity symptoms. The present study selected EF as a representative grass, consisting of five different replacement levels, EF0, EF25, EF50, EF75, and EF100, corresponding to 0%, 25%, 50%, 75%, and 100% of the fermentation substrate, respectively. Simultaneously, in vitro fermentation and the 16S rRNA amplicon sequencing method was used to explore the effect of EF on sheep ruminal fermentation and microbial diversity. The results revealed that EF100 had the highest values for pH, acetate: propionate, the Patescibacteria, Kiritimatiellaeota, and Synergistetes phylum levels, Ruminococcaceae, Prevotellaceae, and Saccharofermentans genus levels than the other treatments (p &lt; 0.05). In contrast, EF25 was associated with higher levels of abundance-based coverage estimator (ACE), Chaol index of the phyla Synergistetes and Bacteroidetes, and of the genus Erysipelotrichaceae, Rikenellaceae, and Prevotella as compared with other treatments (p &lt; 0.05). EF50 resulted in the greatest values for the genus Christensenellaceae and Lachnospiraceae as compared with other treatments (p &lt; 0.05). EF75 resulted in the greatest values for the Shannon index as compared with other treatments (p &lt; 0.05). EF0 resulted in the greatest values for gas production (GP), ammonia nitrogen (NH3-N), total volatile fatty acid (TVFA), acetate, propionate, butyrate, valerate, isobutyrate, isovalerate, and the phyla Firmicutes, Proteobacteria, and Spirochaetes, and the genus Succiniclasticum, Ruminobacter, Family_XIII and Treponema as compared with other treatments (p &lt; 0.05). PICRUSt2 analysis indicated that most of the functional prediction pathways were involved in Carbohydrate metabolism and, Amino acid metabolism. Therefore, the recommended ratio of EF in sheep diet should range from 25% to 50%, and the maximum proportion should not exceed 75%.

A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter

The genus Prevotella comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of Prevotella into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus Prevotella into seven genera, including four novel genera for which the names Segatella, Hoylesella, Leyella and Palleniella are proposed. In addition to the reclassification of Prevotella, this work describes four novel species, Hallella faecis, Xylanibacter rodentium, Xylanibacter muris, and Palleniella intestinalis.

Gut microbiota and short-chain fatty acids may be new biomarkers for predicting neonatal necrotizing enterocolitis: A pilot study.

BackgroundDysbacteriosis is thought to play an important role in the pathogenesis of necrotizing enterocolitis (NEC). We aimed to identify new biomarkers among gut microbiota and short-chain fatty acids (SCFAs) for the early prediction of NEC.Materials and methodsThirty-four preterm infants with gestational ages of ≤ 34 weeks who developed gastrointestinal symptoms were divided into the NEC group (n = 17) and non-NEC group (n = 17). In the NEC group, the gut microbiota and SCFAs in feces were assessed when the infants were enrolled (Group P) and when they were diagnosed with NEC (Group N). In the non-NEC group, samples were assessed when the infants were enrolled (Group C).ResultsThe Ace and Chao1 indices were higher in Group P than in Group C (P < 0.05), and there was no difference between Groups C and N or between Groups P and N (P > 0.05). There was no significant difference in the Simpson and Shannon indices among Groups C, P and N (P > 0.05). The four main phyla showed no differences (P > 0.05) in composition, while at the genus level, compared with Group C, in Group P, Clostridioides, Blautia and Clostridium_sensu_stricto_1 were increased, while Lactobacillus and Bifidobacterium were decreased (P < 0.05). At the species level, Streptococcus salivarius and Rothia mucilaginosa increased, while Bifidobacterium animals subsp. lactis decreased (P < 0.05). In Group N, at the genus level, Stenotrophomonas, Streptococcus and Prevotella increased (P < 0.05). Compared with those in Group C, the levels of acetic acid, propanoic acid and butyric acid decreased significantly in Groups P and N (P < 0.05), and the areas under the curves (AUCs) of these three SCFAs between groups C and P were 0.73, 0.70, and 0.68, respectively.ConclusionThe increase in Streptococcus salivarius and Rothia mucilaginosa and decrease in Bifidobacterium_animals_subsp._lactis, as well as the decrease in acetic, propionic and butyric acids, may help in the early prediction of NEC.

Effects of corn straw treated with CaO on rumen degradation characteristics and fermentation parameters and their correlation with microbial diversity in rumen

The objectives of this study were to investigate the degradation characteristics and fermentation parameters of corn straw treated with different concentrations of calcium oxide (CaO) and degradation characteristics and fermentation parameters of samples in relation to microorganisms diversity in the rumen. Corn straw with 60 % moisture were treated with four concentrations of CaO (0 %, 3 %, 5 %, and 7 % of dry straw weight) respectively: i) The nylon bag technology method was used in estimating the rumen effective degradability, and each treatment was performed eight times. Then, the degradability of dry matter (DM), neutral detergent fiber (NDF) and acid detergent fiber (ADF) were determined by taking nylon bags from rumen at 0 h, 4 h, 8 h, 12 h, 24 h, 48 h and 72 h, respectively. ii) The fermentation parameters of corn straw were measured by rumen simulation technology in vitro. The mixture was measured at different times (6 h, 12 h, 24 h and 72 h) for the determination of ammonia nitrogen (NH3–N), volatile fatty acids (VFAs) indexes and rumen microbes. iii) The free online platform of Majorbio Cloud Platform was used in evaluating microbe diversity, abundance, and taxonomic composition in the rumen. Species difference analysis was designed, each treatment had three replicates, and 48 samples in total were used. iv) The correlations among effective degradability, fermentation indexes, and rumen microorganisms of corn straw treated by CaO were analyzed by means of an online platform. The results showed that i) the effective rumen degradability of corn straw treated with CaO significant differed among treatments (P < 0.01). The degradability of DM, NDF, and ADF in 7 % and 5 % treatments were higher than that in other treatments (P < 0.01). Soluble and rapidly degraded components in corn straw had significant higher in 5 % and 7 % treatments than in the 0 % and 3 % treatments. ii）The concentrations of acetate, propionate, butyrate, and total VFA at 6 h in vitro had significant differences (P < 0.01) or obvious upward tendency with increasing concentration of CaO. iii) Alpha index analysis revealed that rumen microorganisms diversity and abundance obviously decreased from 0 % to 7 % treatment in 6 h fermentation. Rikenellaceae_RC9_gut_group at the genus level decreased in the top 15 species in terms of average abundance (P < 0.01), but the most abundant genus Prevotella_1 had an upward tendency in 6 h incubation (P = 0.066). iv) Correlation analysis demonstrated that Prevotella_1 and Prevotellaceae_UCG-003 had positive correlations with acetate, propionate, total VFA, and DM, NDF, and ADF degradability (P < 0.01). Overall, corn straw treated with CaO at 5 % and 7 % can improve rumen effective degradability and promote the fermentation of corn straw, especially promoting Prevotella_1 enrichment in the straw in a short time. In terms of cost saving, 5 % CaO treatment is the best choice.

Dysbiosis and predicted function of dental and ruminal microbiome associated with bovine periodontitis.

Extensive cattle livestock is advancing in Amazonia and its low productivity, with consequent pressure to open new areas, is partly due to sanitary problems and, among them, the periodontal diseases, whose environmental triggers or modifying factors are unknown. In this study, we used high-throughput sequencing, network analysis and predicted functions to investigate the dental and ruminal microbiota of cattle raised in new livestock areas in the Amazon and identify possible keystone pathogens and proteins associated with the disease. Ninety-three genera were common in dental and ruminal fluid microbiomes and among them periodontal pathogens such as Fusobacterium, Prevotella, Porphyromonas and Actinomyces were recognized. Network analysis showed that dental microbiomes of clinically healthy animals tend to comprise a group of OTUs in homeostasis and when analyzed together, dental and ruminal fluid microbiomes of animals with periodontitis had almost twice the number of negative edges, indicating possible competition between bacteria and dysbiosis. The incisor dental and ruminal fluid microbiomes were dominated by a core community composed of members of the phyla Firmicutes and Bacteroidetes. Network results showed that members of the Prevotella genus stood out among the top five OTUs, with the largest number of hubs in the dental and ruminal microbiota of animals with periodontitis. Protein families linked to an inflammatory environment were predicted in the dental and ruminal microbiota of cattle with periodontitis. The dissimilarity between dental microbiomes, discriminating between healthy cattle and those with periodontitis and the identification of possible key pathogens, represent an important reference to elucidate the triggers involved in the etiopathogenesis of bovine periodontitis, and possibly in the development of measures to control the disease and reduce the pressures for deforestation.