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Frontiers in Veterinary Science 2023The gut microbiomes of equine are plentiful and intricate, which plays an important part in the growth. However, there is a relative lack of information on the microbial...
INTRODUCTION
The gut microbiomes of equine are plentiful and intricate, which plays an important part in the growth. However, there is a relative lack of information on the microbial diversity in the pony's gut.
METHODS
In this article, 118 fecal samples from DeBa pony, NiQi pony and GuZh horse were studied by 16S rRNA amplicon sequencing.
RESULTS
Diversity analysis was used to determine the difference of gut microbiota composition among different breeds. Alpha diversity analysis showed that the gut microbiota of NiQi ponies were abundant and various. Beta diversity analysis showed that the microorganisms constitution of DeBa ponies was more similar to that of NiQi ponies. LDA Effect Size (LEfSe) analysis result that the microorganism biomarkers for NiQi pony at the genus level were Phascolarctobacterium, Paludibacter, and Fibrobacter; the bacterial biomarker for DeBa pony was Streptococcus and Prevotella; and the bacterial biomarkers for GuZh horses was Treponema, Treponema Mogibacterium, Adlercreutzia, and Blautia. The correlation analysis between genera with >1% abundance and horse height found that Streptococcus ( < 0.01), Treponema ( < 0.01), Coprococcus ( < 0.01), Prevotella ( < 0.01), Phascolarctobacterium ( < 0.01), and Mogibacterium ( < 0.01) were significantly associated with horses' height. The functional prediction results indicated that DeBa pony have a microbiota functional more similar to NiQi pony.
DISCUSSION
For the first time, our results announce the species composition and structure of the gut microbiota in Chinese ponies. At the same time, our results can provide theoretical reference for further understanding the healthy breeding, feeding management and disease prevention of horses.
PubMed: 36777669
DOI: 10.3389/fvets.2023.1102186 -
Brazilian Journal of Microbiology :... Jul 2012The aim of the present study was to evaluate the frequency of detection of Mogibacterium timidum in subgingival samples of subjects with generalized aggressive...
The aim of the present study was to evaluate the frequency of detection of Mogibacterium timidum in subgingival samples of subjects with generalized aggressive periodontitis (GAgP) and uncontrolled diabetic and non-diabetic subjects with generalized chronic periodontitis (GChP). 48 patients with GAgP, 50 non-diabetic and 39 uncontrolled (glycated hemoglobin >7%) type 2 diabetic subjects with GChP were enrolled in this study. Subgingival biofilm were collected from deep pockets (probing depth > 7 mm). After DNA extraction, M. timidum was detected by Nested Polymerase Chain Reaction and chi-square test was used to data analysis (p>0.05). There were no differences in the frequency of detection of M. timidum between subjects with GAgP (35%) and non-diabetic subjects with GChP (40%) (p>0.05). The frequency of detection of M. timidum was significantly higher in deep pockets of diabetic subjects with GChP (56%) when compared to GAgP (p<0.05), but similar to non-diabetic subjects with GChP (p>0.05). The frequency of detection of M. timidum was higher in subjects GChP presenting uncontrolled type 2 diabetes mellitus, when compared to GAgP subjects.
PubMed: 24031909
DOI: 10.1590/S1517-838220120003000012 -
Animal : An International Journal of... Mar 2021The caecum is the primary site where microbial fermentation and acidosis occurred. The supplementation of starter feed and alfalfa hay has the potential to influence...
The caecum is the primary site where microbial fermentation and acidosis occurred. The supplementation of starter feed and alfalfa hay has the potential to influence caecal microbiota and then affect caecal fermentation. This study aims to investigate the effect of starter feed and alfalfa hay supplementation on caecal microbiota, immune homeostasis, and growth of preweaning yaks. Twenty 30-day-old male yak calves were randomly assigned to four groups, which separately fed with milk replacer (CON group), milk replacer with alfalfa hay (A group), milk replacer with starter feed (S group), and milk replacer with starter feed plus alfalfa hay (SA group) throughout the trial. Growth performance and plasma physiological and biochemical indicators were measured every 30 days. Calves were sacrificed at 120 days of age. The caecal contents were collected for measuring pH and contents of volatile fatty acids (VFAs) and lipopolysaccharide (LPS) and for characterizing caecal microbiota. The results indicated that individual or simultaneous supplementation with alfalfa hay and starter feed all significantly increased the BW, body height, body length, and chest girth of yak calves. However, supplementation with starter feed significantly increased plasma cortisol, nitric oxide, tumor necrosis factor-α, and interferon-γ concentrations and the ratio of aspartate aminotransferase to alanine aminotransferase of yak calves when compared with the control and alfalfa hay feeding groups, while the co-supplementation of starter feed and alfalfa hay could significantly decrease these inflammation-related indices when compared with the starter feeding group. Sequencing of the 16S rRNA gene showed that starter feed and alfalfa hay separately stimulated the proliferation of starch-decomposing and cellulose- or hemicellulose-decomposing bacteria. This also significantly increased the levels of acetate, propionate, butyrate, valerate, isobutyrate, and isovalerate in the caecal contents. Furthermore, compared with the S and CON groups, the significantly increased genera of Desulfobulbus, Olsenella, Pseudoflavonifractor, and Stomatobaculum in the SA and A groups were beneficial to the immune homeostasis, and the significantly decreased Blautia, Clostridium IV, Bacteroides, Eubacterium, Clostridium XVIII, and Mogibacterium in the SA and A groups were related to the reduced caecal lactate and LPS contents, the decreased inflammatory reaction, and the improved healthy hepatic condition of yak calves. In conclusion, milk replacer supplemented with alfalfa hay and starter feed is recommended during preweaning to improve yak calf health and growth because this regimen promotes the growth and maintains the immune homeostasis of yak calves.
Topics: Animal Feed; Animals; Body Weight; Cattle; Cecum; Diet; Dietary Supplements; Fermentation; Male; Medicago sativa; Microbiota; RNA, Ribosomal, 16S; Rumen; Weaning
PubMed: 33610512
DOI: 10.1016/j.animal.2020.100019 -
Frontiers in Microbiology 2021Current microbiome profiling of type 1 diabetes mellitus (T1D) patients is mostly limited to gut microbiome. We characterized the oral microbiome associated with T1D in...
Current microbiome profiling of type 1 diabetes mellitus (T1D) patients is mostly limited to gut microbiome. We characterized the oral microbiome associated with T1D in children after the onset of the disease and explored its relationship with oral physiological factors and dental status. This cohort study comprised 37 children aged 5-15 years with T1D and 29 healthy children matched in age and gender. Unstimulated whole saliva was collected from diabetic and non-diabetic children, in the morning after brushing their teeth and a fasting period of at least 1 h before sampling. 16S rRNA gene-based analysis was performed by Powersoil Pro kit by Qiagen and Phusion High-Fidelity PCR Master Mix. Oral physiological and dental parameters studied included decayed, missing, and filled teeth index, salivary flow rate, and salivary pH, glucose, calcium, phosphate, and urea levels. Of the identified 105 different genera and 211 different species, the most abundant genera were , , , , and . was more abundant in T1D children. The diabetes group had 22 taxa at the genus level and 33 taxa at the species level that were not present in the control group and the control group exhibited 6 taxa at the genus level and 9 taxa at the species level that did not exist in the diabetes group. In addition, , , and differed between healthy and T1D subjects. Eight species and eight subspecies were significantly more abundant among healthy children than in T1D children. and genera were significantly correlated with salivary parameters. We found similarities between taxa revealed in the present study and those found in gut microbiome in type 1 diabetes mellitus according to gutMDisorder database. Salivary microbiome analysis revealed unique microbial taxa that differed between T1D children and healthy subjects. Several genera found in the saliva of T1D children were associated with gut microbiome in T1D individuals.
PubMed: 34777313
DOI: 10.3389/fmicb.2021.756808 -
PeerJ 2018The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized...
BACKGROUND
The interactions between the gut microbiome and obesity have been extensively studied. Although the oral cavity is the gateway to the gut, and is extensively colonized with microbes, little is known about the oral microbiome in people with obesity. In the present study, we investigated the salivary microbiome in obese and normal weight healthy participants using metagenomic analysis. The subjects were categorized into two groups, obesity and normal weight, based on their BMIs.
METHODS
We characterized the salivary microbiome of 33 adults with obesity and 29 normal weight controls using high-throughput sequencing of the V3-V4 region of the 16S rRNA gene (Illumina MiSeq). None of the selected participants had systemic, oral mucosal, or periodontal diseases.
RESULTS
The salivary microbiome of the obesity group was distinct from that of the normal weight group. The salivary microbiome of periodontally healthy people with obesity had both significantly lower bacterial diversity and richness compared with the controls. The genus , , and were significantly more abundant in the obesity group; meanwhile the genus , and were less abundant in the obesity group. We also performed a functional analysis of the inferred metagenomes, and showed that the salivary community associated with obesity had a stronger signature of immune disease and a decreased functional signature related to environmental adaptation and Xenobiotics biodegradation compared with the normal weight controls.
DISCUSSION
Our study demonstrates that the microbial diversity and structure of the salivary microbiome in people with obesity are significantly different from those of normal weight controls. These results suggested that changes in the structure and function of salivary microbiome in people with obesity might reflect their susceptibility to oral diseases.
PubMed: 29576948
DOI: 10.7717/peerj.4458 -
Animal Microbiome Mar 2022Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. The role of the gut microbiota in...
BACKGROUND
Helminth parasitism is a world-wide problem in livestock industries, with major impacts on health, welfare and productivity. The role of the gut microbiota in host-helminth interactions in ruminants has been extensively examined and the present study added to this body of knowledge by assessing the effects of resistance and susceptibility to helminth infection in the gastro-intestinal tract (GIT). Australian Sheep Breeding Values (ASBVs) for faecal egg count (FEC) were used to select the 10 highly helminth-susceptible (High-FEC) and 10 highly helminth-resistant (Low-FEC) sheep. FEC status was confirmed during the experiment. Using samples from the faeces and the lumen of the rumen, abomasum, duodenum, jejunum, ileum, caecum, and colon, DNA was extracted and used for 16 rRNA gene amplicon sequencing.
RESULTS
The most frequent genera identified along the GIT were Eubacterium, Oscillibacter, and Ruminococcus. Intersectoral-specialization zones were identified along the GIT, with the duodenum displaying major differences between the High-FEC and Low-FEC animals in values for alpha and beta diversity. After taking all samples into account and adjusting for GIT segment, the High-FEC and Low-FEC sheep differed significantly for four genera Butyrivibrio, Mycoplasma, Lachnoclostridium and Succiniclasticum. In the duodenum, the abundances of Aminipila, Lachnoclostridium and Mogibacterium differed significantly between the High-FEC and Low-FEC sheep. In the ileum, on the other hand, the genus Mycoplasma was significantly depleted in the Low-FEC group.
CONCLUSIONS
The gastro-intestinal microbial profile varies widely between helminth-resistant and helminth-susceptible sheep. Each GIT section appears to support a particular bacterial composition leading to inter-sectoral differences among the various microbial communities. The microbial populations were most rich and diverse in the duodenum of helminth-resistant sheep, comprising bacterial genera that generally ferment carbohydrates. This observation suggests that helminth-resistant sheep can reorganize the duodenal microbiome taxa which may restrict the development of parasites.
PubMed: 35287759
DOI: 10.1186/s42523-022-00172-1 -
PeerJ 2020The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible...
BACKGROUND
The gut microbiome and microbiome-gut-brain (MGB) axis have been receiving increasing attention for their role in the regulation of mental behavior and possible biological basis of psychiatric disorders. With the advance of next-generation sequencing technology, characterization of the gut microbiota in schizophrenia (SZ) patients can provide rich clues for the diagnosis and prevention of SZ.
METHODS
In this study, we compared the differences in the fecal microbiota between 82 SZ patients and 80 demographically matched normal controls (NCs) by 16S rRNA sequencing and analyzed the correlations between altered gut microbiota and symptom severity.
RESULTS
The alpha diversity showed no significant differences between the NC and SZ groups, but the beta diversity revealed significant community-level separation in microbiome composition between the two groups (pseudo- =3.337, < 0.001, uncorrected). At the phylum level, relatively more and less ( < 0.05, FDR corrected) were found in the SZ group. At the genus level, the relative abundances of , , , , , undefined and undefined were significantly increased, whereas the abundances of , , and were decreased in the SZ group compared to the NC group ( < 0.05, FDR corrected). We performed PICRUSt analysis and found that several metabolic pathways differed significantly between the two groups, including the Polyketide sugar unit biosynthesis, Valine, Leucine and Isoleucine biosynthesis, Pantothenate and CoA biosynthesis, C5-Branched dibasic acid metabolism, Phenylpropanoid biosynthesis, Ascorbate and aldarate metabolism, Nucleotide metabolism and Propanoate metabolism pathways ( < 0.05, FDR corrected). Among the SZ group, the abundance of was positively correlated with the total Positive and Negative Syndrome Scale (PANSS) scores ( = 0.24, < 0.05, uncorrected) as well as the general PANSS scores ( = 0.22, < 0.05, uncorrected); was negatively related to the negative scores of PANSS ( = 0.22, < 0.05, uncorrected).
CONCLUSIONS
Our findings provided evidence of altered gut microbial composition in SZ group. In addition, we found that and were associated with the severity of symptoms for the first time, which may provide some new biomarkers for the diagnosis of SZ.
PubMed: 32821537
DOI: 10.7717/peerj.9574 -
Biology of Blood and Marrow... Nov 2020Infection is a major cause of morbidity and mortality after hematopoietic cell transplantation (HCT). Gut microbiota (GM) composition and metabolites provide...
Infection is a major cause of morbidity and mortality after hematopoietic cell transplantation (HCT). Gut microbiota (GM) composition and metabolites provide colonization resistance against dominance of potential pathogens, and GM dysbiosis following HCT can be deleterious to immune reconstitution. Little is known about the composition, diversity, and evolution of GM communities in HCT patients and their association with subsequent febrile neutropenia (FN) and infection. Identification of markers before HCT that predict subsequent infection could be useful in developing individualized antimicrobial strategies. Fecal samples were collected prospectively from 33 HCT recipients at serial time points: baseline, post-conditioning regimen, neutropenia onset, FN onset (if present), and hematologic recovery. GM was assessed by 16S rRNA sequencing. FN and major infections (ie, bloodstream infection, typhlitis, invasive fungal infection, pneumonia, and Clostridium difficile enterocolitis) were identified. Significant shifts in GM composition and diversity were observed during HCT, with the largest alterations occurring after initiation of antibiotics. Loss of diversity persisted without a return to baseline at hematologic recovery. GM in patients with FN was enriched in Mogibacterium, Bacteroides fragilis, and Parabacteroides distasonis, whereas increased abundance of Prevotella, Ruminococcus, Dorea, Blautia, and Collinsella was observed in patients without fever. A baseline protective GM profile (BPGMP) was predictive of protection from major infection. The BPGMP was associated with subsequent major infections with 77% accuracy and an area under the curve of 79%, with sensitivity, specificity, and positive and negative predictive values of 0.71, 0.91, 0.77, and 0.87, respectively. Our data show that large shifts in GM composition occur early after HCT, and differences in baseline GM composition are associated with the development of subsequent major infections.
Topics: Bacteroidetes; Feces; Gastrointestinal Microbiome; Hematopoietic Stem Cell Transplantation; Humans; RNA, Ribosomal, 16S
PubMed: 32717434
DOI: 10.1016/j.bbmt.2020.07.023 -
Scientific Reports Feb 2023While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have...
While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.
Topics: Sheep; Animals; Cattle; Archaea; RNA, Ribosomal, 16S; Plant Breeding; Veillonellaceae; Campylobacter; Clostridiales
PubMed: 36849493
DOI: 10.1038/s41598-023-28909-1 -
Frontiers in Cellular and Infection... 2022The Orang Asli (OA) of Malaysia have been relatively understudied where little is known about their oral and gut microbiomes. As human health is closely intertwined with...
The Orang Asli (OA) of Malaysia have been relatively understudied where little is known about their oral and gut microbiomes. As human health is closely intertwined with the human microbiome, this study first assessed the cardiometabolic health in four OA communities ranging from urban, rural to semi-nomadic hunter-gatherers. The urban Temuan suffered from poorer cardiometabolic health while rural OA communities were undergoing epidemiological transition. The oral microbiota of the OA were characterised by sequencing the V4 region of the 16S rRNA gene. The OA oral microbiota were unexpectedly homogenous, with comparably low alpha diversity across all four communities. The rural Jehai and Temiar PP oral microbiota were enriched for uncharacterised bacteria, exhibiting potential for discoveries. This finding also highlights the importance of including under-represented populations in large cohort studies. The Temuan oral microbiota were also elevated in opportunistic pathogens such as , and , suggesting possible oral dysbiosis in these urban settlers. The semi-nomadic Jehai gut microbiota had the highest alpha diversity, while urban Temuan exhibited the lowest. Rural OA gut microbiota were distinct from urban-like microbiota and were elevated in bacteria genera such as , Lachnospiraceae ND3007, and Urban Temuan microbiota were enriched in and Ruminococcacecae UCG-013. This study brings to light the current health trend of these indigenous people who have minimal access to healthcare and lays the groundwork for future, in-depth studies in these populations.
Topics: Bacteria; Cardiovascular Diseases; Gastrointestinal Microbiome; Humans; Microbiota; RNA, Ribosomal, 16S
PubMed: 35531342
DOI: 10.3389/fcimb.2022.812345