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Veterinary Sciences Nov 2022Here, we present a taxonomically defined fecal microbiome dataset for healthy domestic cats (Felis catus) fed a range of commercial diets. We used this healthy reference...
Here, we present a taxonomically defined fecal microbiome dataset for healthy domestic cats (Felis catus) fed a range of commercial diets. We used this healthy reference dataset to explore how age, diet, and living environment correlate with fecal microbiome composition. Thirty core bacterial genera were identified. Prevotella, Bacteroides, Collinsella, Blautia, and Megasphaera were the most abundant, and Bacteroides, Blautia, Lachnoclostridium, Sutterella, and Ruminococcus gnavus were the most prevalent. While community composition remained relatively stable across different age classes, the number of core taxa present decreased significantly with age. Fecal microbiome composition varied with host diet type. Cats fed kibble had a slightly, but significantly greater number of core taxa compared to cats not fed any kibble. The core microbiomes of cats fed some raw food contained taxa not as highly prevalent or abundant as cats fed diets that included kibble. Living environment also had a large effect on fecal microbiome composition. Cats living in homes differed significantly from those in shelters and had a greater portion of their microbiomes represented by core taxa. Collectively our work reinforces the findings that age, diet, and living environment are important factors to consider when defining a core microbiome in a population.
PubMed: 36423084
DOI: 10.3390/vetsci9110635 -
Zhongguo Dang Dai Er Ke Za Zhi =... Dec 2022To study the structure and diversity of gut microbiota in children with autism spectrum disorder (ASD), and to predict the metabolic function of gut microbiota.
OBJECTIVES
To study the structure and diversity of gut microbiota in children with autism spectrum disorder (ASD), and to predict the metabolic function of gut microbiota.
METHODS
Fecal samples were collected from 30 ASD children (ASD group) and 20 typically developing (TD) children (TD group). Genomic DNA was extracted, the 16S rDNA V4 region was amplified by PCR, and Illumina NovaSeq6000 platform was used for high-throughput sequencing. The composition and distribution characteristics of gut microbiota were analyzed for the two groups, and the metabolic function of gut microbiota was predicted.
RESULTS
There were no significant differences in alpha diversity indices (Chao1, Shannon, and Simpson) of gut microbiota between the ASD and TD groups (>0.05). At the phylum and class levels, there was no significant difference in the structure of gut microbiota between the two groups (>0.05). Compared with the TD group, the ASD group had significantly higher abundance of Megamonas, Barnesiella, Dialister, Megasphaera, Ruminococcus_torques_group, and Fusobacterium at the genus level (<0.05). Functional prediction analysis showed that compared with the TD group, the ASD group had a significantly lower abundance of the gut microbiota with the metabolic functions such as tryptophan degradation, glutamate degradation, and butyrate production (<0.05) and a significantly higher abundance of the gut microbiota with the metabolic function of GABA degradation (<0.05).
CONCLUSIONS
There is no significant difference in the alpha diversity of gut microbiota between ASD children and TD children, while there are differences in the composition of species at the genus level and the metabolic functions of gut microbiota.
Topics: Humans; Child; Gastrointestinal Microbiome; Autism Spectrum Disorder; Bacteria; Feces; Butyrates
PubMed: 36544419
DOI: 10.7499/j.issn.1008-8830.2207130 -
PloS One 2022The objective of this study was to evaluate the effect of essential oils plus dry herbs (PHYTO) and encapsulated sodium butyrate (BUT) supplementation compared with...
The objective of this study was to evaluate the effect of essential oils plus dry herbs (PHYTO) and encapsulated sodium butyrate (BUT) supplementation compared with enramycin (ENR), as a growth promoter, on the performance, diarrhoea control and intestinal microbiota in lightly weaned piglets. Two hundred weaned piglets, 20 days old, 4.69 ± 0.56 kg, were submitted during the nursery phase (20 to 69 days of age) to four treatments: control (CTR)-without any additive supplementation; ENR (with 8 ppm of enramycin throughout), BUT (with 2000 ppm between 20 to 34 d, 1500 ppm between 34 to 48 d and 1000 ppm between 48 to 69 d), and PHYTO (150 ppm between 20 to 48 d). At 62 days old, forty piglets (10 replicates per treatment) were slaughtered to perform bacterial identification through 16S rRNA (V3-V4) sequencing of the caecal content. During the second phase of the trial (34 to 48 days), the BUT group showed higher DWG (P = 0.023) and BW (P = 0.039) than the CTR group, and all groups that received additives had better FCR than the CTR group (P = 0.001). In the last phase of the trial (48 to 69 days), the ENR group presented a better FCR (P = 0.054) than the CRT and other groups. In the total period (20 to 69 days), ENR and BUT showed better FCR (P = 0.006) than CRT. Diarrhoea incident data showed differences (P<0.05), favouring the BUT treatment compared to the CTR. Only the Megasphaeraceae and Streptococcaceae families showed differences (p<0.05) in relative abundance between CTR and PHYTO and between CTR and BUT, respectively. Differential abundances of the Megasphaera and Streptococcus genera were observed between CTR and PHYTO and CTR and BUT. Phytogenics and encapsulated sodium butyrate are able and effective for modulating the specific caecal microbiota, improving performance and controlling diarrhoea occurrence.
Topics: Animals; Anti-Bacterial Agents; Butyric Acid; Diarrhea; Diet; RNA, Ribosomal, 16S; Swine
PubMed: 36548241
DOI: 10.1371/journal.pone.0279197 -
Animals : An Open Access Journal From... Nov 2023This study was conducted to investigate the effects of feeding oregano essential oil, butyrate, and its mixture on the intestinal microbial diversity of calves. A...
This study was conducted to investigate the effects of feeding oregano essential oil, butyrate, and its mixture on the intestinal microbial diversity of calves. A completely randomized experimental design was used. Sixty-four healthy neonatal Holstein female calves with birth weight ≥ 35 kg were randomly divided into one control and three treatments (16 calves per group). The control group was fed normally, and the treatment group was fed oregano essential oil, butyrate, and their mixture, respectively. The experiment lasted for 70 days, and the lactation period lasted for 56 days. On days 55 and 70, rectal fecal samples from five calves were collected from each group for 16S rRNA amplification and sequencing. The results showed as follows: (1) the three treatments had no significant effects on the intestinal microbial community diversity, community uniformity, and community pedigree diversity of calves ( > 0.05). (2) At the phylum level, Firmicutes, Bacteroidota, Spriochatetota, Actinobacteriota, Firmicutes, and Bacteroidota gates of the main bacteria were detected in feces. (3) At the genus level, the top ten species with relative abundance detected are: , , , , , , , , and , . (4) LEfSe analysis results show that the species with significant differences in the control group were , , , and , ; in the essential oil group were , , , and ; in the sodium butyrate group were , , ; in the mixed group were , . (5) The functional prediction analysis of calf gut microbes, found on the KEGG pathway2, shows that essential oil significantly improved membrane transport, Sodium butyrate inhibits lipid metabolism and improves the body's resistance to disease. ( < 0.05). (6) The effects of each treatment on the intestinal microbial structure of calves did not last for 14 days after the treatment was stopped. In conclusion, the addition of oregano essential oil, butyrate, and its mixtures to milk fed to calves can modulate the microbial structure, and it is recommended that oregano essential oil and butyrate be used separately, as a mixture of the two can increase the rate of diarrhea in calves.
PubMed: 38003141
DOI: 10.3390/ani13223523 -
Microorganisms Jan 2024The Gram-negative, strictly anaerobic bacterium was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use... (Review)
Review
The Gram-negative, strictly anaerobic bacterium was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of to produce C-C carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.
PubMed: 38276203
DOI: 10.3390/microorganisms12010219 -
Frontiers in Microbiology 2023Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many...
Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens and were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as , , , , , and were found to be enriched in response to social stress. In contrast, the genera , , , , , , and were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are and , as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of and . Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.
PubMed: 38029169
DOI: 10.3389/fmicb.2023.1197371 -
Signal Transduction and Targeted Therapy May 2021COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity....
COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients, 29 influenza B patients, and 28 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium, Rothia, and Streptococcus. Based on the relative abundance of the oropharyngeal microbiome, we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889, in which Veillonella was identified as the most prominent biomarker for COVID-19 group. Several members of the genus Veillonella, especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients, were also overrepresented in the BALF of COVID-19 patients, indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients. We also found the increased ratios of Klebsiella sp., Acinetobacter sp., and Serratia sp. were correlated with both disease severity and elevated systemic inflammation markers (neutrophil-lymphocyte ratio, NLR), suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response. Moreover, the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism. In addition, all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group, and were significantly enriched in critical cases. In conclusion, we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.
Topics: Adult; Bacteria; COVID-19; Female; Humans; Male; Metagenomics; Microbiota; Middle Aged; Oropharynx; SARS-CoV-2
PubMed: 33986253
DOI: 10.1038/s41392-021-00614-3 -
Animal Nutrition (Zhongguo Xu Mu Shou... Mar 2021This review aims to give an overview of the efficacy of yeast supplementation on growth performance, rumen pH, rumen microbiota, and their relationship to meat and milk... (Review)
Review
This review aims to give an overview of the efficacy of yeast supplementation on growth performance, rumen pH, rumen microbiota, and their relationship to meat and milk quality in ruminants. The practice of feeding high grain diets to ruminants in an effort to increase growth rate and weight gain usually results in excess deposition of saturated fatty acids in animal products and increased incidence of rumen acidosis. The supplementation of yeast at the right dose and viability level could counteract the acidotic effects of these high grain diets in the rumen and positively modify the fatty acid composition of animal products. Yeast exerts its actions by competing with lactate-producing ( and ) bacteria for available sugar and encouraging the growth of lactate-utilising bacteria (). is known to convert lactate into butyrate and propionate leading to a decrease in the accumulation of lactate thereby resulting in higher rumen pH. Interestingly, this creates a conducive environment for the proliferation of vaccenic acid-producing bacteria () and ciliate protozoa, both of which have been reported to increase the ruminal concentration of -11 and -9, -11-conjugated linoleic acid (CLA) at a pH range between 5.6 and 6.3. The addition of yeast into the diet of ruminants has also been reported to positively modify rumen biohydrogenation pathway to synthesise more of the beneficial biohydrogenation intermediates ( 11 and 9, 11). This implies that more dietary sources of linoleic acid, linolenic acid, and oleic acid along with beneficial biohydrogenation intermediates (-9, -11-CLA, and -11) would escape complete biohydrogenation in the rumen to be absorbed into milk and meat. However, further studies are required to substantiate our claim. Therefore, techniques like transcriptomics should be employed to identify the mRNA transcript expression levels of genes like stearoyl-CoA desaturase fatty acid synthase, and elongase of very long chain fatty acids 6 in the muscle. Different strains of yeast need to be tested at different doses and viability levels on the fatty acid profile of animal products as well as its vaccenic acid and rumenic acid composition.
PubMed: 33997329
DOI: 10.1016/j.aninu.2020.10.005 -
Veterinary Sciences Nov 2023In order to study the effects of a low protein diet on the production performance and intestinal microbiota composition of Hexi pigs, twenty-seven Hexi pigs with an...
In order to study the effects of a low protein diet on the production performance and intestinal microbiota composition of Hexi pigs, twenty-seven Hexi pigs with an initial body weight of 60.50 ± 2.50 kg were randomly divided into three groups (control group (CG), group 1 (G1), and group 2 (G2)) and participated in a 60-day finishing trial. The CG was fed a normal protein level diet with a protein level of 16.0%, and G1 and G2 were fed a low protein level diet with protein levels of 14.0% and 12.0%, respectively. The results showed that the low protein level diet had no significant effect on the production performance of Hexi pigs, compared with the CG, the slaughter rate of G1 and G2 increased by 2.49% ( > 0.05) and 6.18% ( > 0.05), the shear force decreased by 2.43% ( > 0.05) and 15.57% ( > 0.05), the cooking loss decreased by 24.02% ( < 0.05) and 21.09% ( > 0.05), and the cooking percentage increased by 13.20% ( > 0.05) and 11.59% ( > 0.05). From 45 min to 24 h and 48 h after slaughter, each group of pH decreased by 1.02, 0.66, and 0.42. For muscle flesh color, the lightness (L) increased by 13.31% ( > 0.05) and 18.01% ( > 0.05) in G1 and G2 and the yellowness (b) increased by 7.72% ( > 0.05) and 13.06% ( > 0.05). A low protein level diet can improve the intestinal flora richness and diversity of growing and finishing pigs. In the jejunum, the ACE index (899.95), Simpson index (0.90), and Shannon (4.75) index were higher in G1 than in the other groups, but the Chao1 index (949.92) was higher in G2 than in the remaining two groups. Proteobacteria, Actinobacteria, Euryarchaeota, and Verrucomicrobia were significantly higher in G1 than in the CG. The relative abundances of , , and in G1 was significantly higher than in the CG ( < 0.05). In the cecum, the ACE index (900.93), Chao1 index (879.10), Simpson index (0.94), and Shannon (5.70) index were higher in G1 than in the remaining groups. The Spirochaetes in G2 were significantly higher than in the other groups, but the Verrucomicrobia was significantly lower than in the other groups. The relative abundances of were higher in G1 and G2 than in the CG ( > 0.05). The relative abundances of unidentified_Clostridiales and in G2 were significantly lower than in the CG ( < 0.05). The relative abundance of Turicibacter in G1 was significantly lower than in the CG ( < 0.05). The relative abundances of other bacterial genera in G1 and G2 were increased by 30.81% ( > 0.05) and 17.98% ( > 0.05).
PubMed: 37999478
DOI: 10.3390/vetsci10110655 -
The Journal of Infectious Diseases Mar 2021Vaginal yeast is frequently found with Lactobacillus-dominant microbiota. The relationship between vaginal yeast and other bacteria has not been well characterized.
BACKGROUND
Vaginal yeast is frequently found with Lactobacillus-dominant microbiota. The relationship between vaginal yeast and other bacteria has not been well characterized.
METHODS
These analyses utilized data from the Preventing Vaginal Infections trial. Relative abundance of vaginal bacteria from 16S ribosomal ribonucleic acid gene amplicon sequencing and quantities of 10 vaginal bacteria using taxon-directed polymerase chain reaction assays were compared at visits with and without detection of yeast on microscopy, culture, or both.
RESULTS
Higher relative abundances of Megasphaera species type 1 (risk ratio [RR], 0.70; 95% confidence interval [CI], 0.52-0.95), Megasphaera species type 2 (RR, 0.81; 95% CI, 0.67-0.98), and Mageeibacillus indolicus (RR, 0.46; 95% CI, 0.25-0.83) were associated with lower risk of detecting yeast. In contrast, higher relative abundances of Bifidobacterium bifidum, Aerococcus christensenii, Lactobacillus mucosae, Streptococcus equinus/infantarius/lutentiensis, Prevotella bivia, Dialister propionicifaciens, and Lactobacillus crispatus/helveticus were associated with yeast detection. Taxon-directed assays confirmed that increasing quantities of both Megasphaera species and M indolicus were associated with lower risk of detecting yeast, whereas increasing quantities of L crispatus were associated with higher risk of detecting yeast.
CONCLUSIONS
Despite an analysis that examined associations between multiple vaginal bacteria and the presence of yeast, only a small number of vaginal bacteria were strongly and significantly associated with the presence or absence of yeast.
Topics: Bacteria; Female; Humans; Megasphaera; Microbiota; RNA, Ribosomal, 16S; Vagina; Vaginosis, Bacterial; Yeasts
PubMed: 32726445
DOI: 10.1093/infdis/jiaa459