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Animals : An Open Access Journal From... Apr 2022The ocular microbiome in horses is poorly described compared to other species, and most of the information available in the literature is based on traditional...
The ocular microbiome in horses is poorly described compared to other species, and most of the information available in the literature is based on traditional techniques, which has limited the depth of the knowledge on the subject. The objective of this study was to characterize and predict the metabolic pathways of the ocular microbiome of a group of healthy horses. Conjunctival swabs were obtained from both eyes of 14 horses, and DNA extraction was performed from the swabs, followed by next generation sequencing and bioinformatics analyses employing DADA2 and PICRUSt2. A total of 17 phyla were identified, of which () was the most abundant (59.88%), followed by () (22.44%) and () (16.39%), totaling an average of 98.72% of the communities. Similarly, of the 278 genera identified, , , , , and were present in more than 5% of the samples analyzed. Both and showed great heterogeneity within the samples. The most abundant inferred metabolic functions were related to vital functions for bacteria such as aerobic respiration, amino acid, and lipid biosynthesis.
PubMed: 35454190
DOI: 10.3390/ani12080943 -
PloS One 2021Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and...
Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and production traits, but published results are difficult to reproduce due to large sources of variation. The objectives of this study were to evaluate the associations of ruminal microbiota and its association with genetic lines selected by somatic cell score (SCS) or milk persistency (PERS), as well as milk production, somatic cell score, fat and protein contents, and fatty acids and proteins of milk, using the principles of compositional data. A large sample of 700 Lacaune dairy ewes from INRAE La Fage feeding the same diet and belonging to two divergent genetic lines selected for SCS or PERS was used. The ruminal bacterial metagenome was sequenced using the 16S rRNA gene, resulting in 2,059 operational taxonomic units affiliated with 112 genera. The abundance data were centred log-transformed after the replacement of zeros with the geometric Bayesian method. Discriminant analysis of the SCS showed differences between SCS+ and SCS- ewes, while for PERS no difference was obtained. Milk traits as fat content, protein content, saturated fatty acids and caseins of milk were negatively associated with Prevotella (R = [-0.08;-0.16]), Suttonella (R = [-0.09;-0.16]) and Ruminococcus (R = [-0.08;-0.16]), and positively associated with Lachnospiraceae (R = [0.09;0.16]) and Christensenellaceae (R = [0.09;0.16]). Our findings provide an understanding of the application of compositional data to microbiome analysis, and the potential association of Prevotella, Suttonella, Ruminococcaceae and Lachnospiraceae with milk production traits such as milk fatty acids and proteins in dairy sheep.
Topics: Animals; Bacteria; Bayes Theorem; Diet; Fatty Acids; Female; Lactation; Metagenome; Microbiota; Milk; RNA, Ribosomal, 16S; Rumen; Sheep
PubMed: 34310617
DOI: 10.1371/journal.pone.0254874 -
Frontiers in Microbiology 2022Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In...
Bacteria play an essential role in the health of marine mammals, and the bacteria of marine mammals are widely concerned, but less is known about freshwater mammals. In this study, we investigated the bacteria of various body sites of Yangtze finless porpoise () and analyzed their association with freshwater environmental bacteria. The bacterial community and function of Yangtze finless porpoise showed apparent site-specificity. Various body sites have distinct differences in bacteria and have their dominant bacteria. , , , dominated in the intestine (fecal and rectal samples). , , and dominated in the oral. The dominant genera in the blowhole include , , and two uncultured genera. , , and were dominant in the skin. The alpha diversity of intestinal (fecal and rectal) bacteria was the lowest, while that of skin was the highest. The oral and skin bacteria of Yangtze finless porpoise significantly differed between the natural and semi-natural conditions, but no sex difference was observed. A clear boundary was found between the animal and the freshwater environmental bacteria. Even the skin bacteria, which are more affected by the environment, are significantly different from the environmental bacteria and harbor indigenous bacteria. Our results provide a comprehensive preliminary exploration of the bacteria of Yangtze finless porpoise and its association with bacteria in the freshwater environment.
PubMed: 36605503
DOI: 10.3389/fmicb.2022.1006251 -
Frontiers in Veterinary Science 2022Several episodes of increased mortality in wild birds of the families and have been documented in recent decades. The majority of affected animals exhibited...
Several episodes of increased mortality in wild birds of the families and have been documented in recent decades. The majority of affected animals exhibited necrotizing pneumonia with intralesional bacteria. (.) , a gram-negative bacterium in the family, has been regularly cultured bacteriologically from affected birds and has long been suspected as a potentially fatal cause of respiratory disease in birds. However, a direct causal relationship between this specific bacterium and the observed lesions within birds has not yet been established. Therefore, postmortem tissue from six tits was used in the present study, including three blue tits () and three great tits (). Five of the six tits tested positive for in bacteriological examination and originated from two incidents of increased mortality in in Germany. Animals found dead in the administrative district of Arnsberg (North Rhine Westphalia) in 2018 and 2020 were investigated for genomic fragments of by chromogenic hybridization using a newly developed DNA probe based on publicly assessable DNA sequences of the 16S rRNA gene of . Positive hybridization signals were detected in five out of five animals and were predominantly detected within necrotizing lesions in lung and occasionally in lesions affecting liver and trachea. Interestingly, the lung of one animal without obvious necrotizing pulmonary lesions revealed positive hybridization results in the lumen of one pulmonary blood vessel. Two negative controls, including one bacteriologically -negative great tit and a cattle egret () suffering from salmonellosis, did not yield positive signals, indicating high sensitivity and specificity of the probe used. This is the first time that has been clearly identified within necrotizing lesions in deceased tits. Although Koch's postulates have yet to be fulfilled, positive hybridization signals in association with detectable lesions are considered as further and strong evidence of the significant contribution of to the several episodes of tit mortality recorded in Germany.
PubMed: 36157175
DOI: 10.3389/fvets.2022.977570 -
Journal of Animal Science Sep 2018The objective of this study was to evaluate the changes in the ruminal fermentation, epithelium-associated microbiota, and ruminal epithelial barrier function in...
The objective of this study was to evaluate the changes in the ruminal fermentation, epithelium-associated microbiota, and ruminal epithelial barrier function in response to severe feed restriction (SFR) in pregnant ewes. Sixteen pregnant ewes (108 d of gestation) were randomly blocked and assigned to 1 of 2 treatments: control (CON, n = 8) and SFR (n = 8). Ewes were fed a common diet with a 60:40 forage to concentrate ratio for 7-d baseline period followed by a SFR challenge period. Ewes on the SFR treatment were restricted to 30% of the base for 15 d. At the end of the experimental period, all animals were slaughtered and then ruminal contents and ruminal epithelial tissue were collected. Results showed that ruminal pH was greater in SFR group (P = 0.040) compared with CON group, while SFR decreased (P < 0.05) the concentrations of ruminal acetate, propionate, butyrate, and total volatile fatty acid. A plot of principal coordinate analysis and analysis of molecular variance revealed that the composition of ruminal epithelial bacterial communities in the CON group was distinct from that of the ruminal epithelial microbiome in the SFR animals. At the genus level, SFR increased the abundance of unclassified Neisseriaceae, Comamonas, and Papillibacter, and decreased the proportion of Howardella, Desulfobulbus, and Suttonella (P < 0.05) compared with CON group. The metagenome of ruminal epithelium-associated microbiota predicted by PICRUSt revealed that the SFR significantly affected 14 metabolic pathways, and 9 were significantly enriched in the SFR group. In particular, SFR markedly increased relative abundances of dominant gene families involved in amino acid metabolism (P = 0.003), cellular processes and signaling (P = 0.021), and lipid metabolism (P = 0.001). The real-time PCR results showed SFR decreased the mRNA expression of IL-10 (P = 0.003) and upregulated the mRNA expression of IL-6 (P = 0.003) and TLR4 (P = 0.021). The mRNA expression of Claudin-1 (P = 0.001) and ZO-1 (P = 0.009) were lower in the SFR group compared with the CON group. Generally, our data suggest that SFR decreased most ruminal fermentation parameters, altered the composition of rumen epithelium-associated microbiota, and compromised the barrier function of rumen epithelium. These findings are of great importance for understanding the alteration in the rumen function following SFR in pregnant ewes.
Topics: Animal Feed; Animals; Butyrates; Diet; Epithelium; Fatty Acids, Volatile; Female; Fermentation; Food Deprivation; Microbiota; Pregnancy; Propionates; Random Allocation; Rumen; Sheep
PubMed: 30272228
DOI: 10.1093/jas/sky306 -
Genome Announcements Feb 2017We report here the draft genome sequence of the bacterium. To date, this bacterium, found in birds, passed only phylogenetic and phenotypic analyses. To our knowledge,...
We report here the draft genome sequence of the bacterium. To date, this bacterium, found in birds, passed only phylogenetic and phenotypic analyses. To our knowledge, this is the first publication of the genome sequence. The genetic profile provides a basis for further analysis of its infection pathways.
PubMed: 28209820
DOI: 10.1128/genomeA.01592-16 -
Microbial Ecology May 2023Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt...
Bonelli's eagle (Aquila fasciata) is an endangered raptor species in Europe, and trichomonosis is one of the menaces affecting chicks at nest. In this paper, we attempt to describe the oral microbiome of Bonelli's eagle nestlings and evaluate the influence of several factors, such as captivity breeding, Trichomonas gallinae infection, and the presence of lesions at the oropharynx. The core oral microbiome of Bonelli's eagle is composed of Firmicutes, Bacteroidota, Fusobacteria and Proteobacteria as the most abundant phyla, and Megamonas and Bacteroides as the most abundant genera. None of the factors analysed showed a significant influence on alfa diversity, but beta diversity was affected for some of them. Captivity breeding exerted a high influence on the composition of the oral microbiome, with significant differences in the four most abundant phyla, with a relative increase of Proteobacteria and a decrease of the other three phyla in comparison with chicks bred at nest. Some genera were more abundant in captivity bred chicks, such as Escherichia-Shigella, Enterococcus, Lactobacillus, Corynebacterium, Clostridium and Staphylococcus, while Bacteroides, Oceanivirga, Peptostreptococcus, Gemella, Veillonella, Mycoplasma, Suttonella, Alloscardovia, Varibaculum and Campylobacter were more abundant in nest raised chicks. T. gallinae infection slightly influenced the composition of the microbiome, but chicks displaying trichomonosis lesions had a higher relative abundance of Bacteroides and Gemella, being the last one an opportunistic pathogen of abscess complications in humans. Raptor's microbiomes are scarcely studied. This is the first study on the factors that influence the oral microbiome of Bonelli's eagle.
Topics: Animals; Humans; Trichomonas; Eagles; Europe
PubMed: 35385973
DOI: 10.1007/s00248-022-02002-y -
MSystems Feb 2024Ruminal microbiota is gradually established after birth, while microbiota maturation could be highly diverse because of varied solid dietary accessibility. However, how...
Ruminal microbiota is gradually established after birth, while microbiota maturation could be highly diverse because of varied solid dietary accessibility. However, how the ruminal microbiota accreted from postnatal hay diets alters rumen epithelial development, and how this affects animal health remains largely unknown. Here, neonatal lambs were introduced to starchy corn-soybean starter or corn-soybean starter + alfalfa hay (AH) to investigate the influences of early life ruminal microbiome on rumen epithelial development using integrated 16s rRNA sequencing-metagenome-transcriptome approaches. The results showed that AH introduction elevated average daily weight gain, rumen weight and volume, rumen epithelial papillae length, and rumen muscle layer thickness. Meanwhile, the relative abundance of fibrolytic bacteria ( R-7 group, UCG-001, and ), acetate producer ( and and propionate producer was increased in the rumen content by AH supplementation ( < 0.05). Moreover, AH introduction decreased the relative abundance of total CAZymes, CBM, and GH and increased the abundance of KO genes related to volatile fatty acid (VFA) generation in the rumen content. AH lambs had a higher relative abundance of , , and ( < 0.05), while a lower relative abundance of , , , , , and ( < 0.05) in the rumen epithelial samples. Furthermore, these alterations in ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation. In summary, AH introduction benefited ruminal fiber degradation and VFA generation bacteria colonization and promoted ruminal epithelial development. These findings provide new insights into ruminal microbial-host interactions in the early life.IMPORTANCEWhile it is established that a fiber-rich diet promotes rumen development in lambs, further research is needed to investigate the precise response of rumen microbiota and epithelium to high-quality alfalfa hay. Here, we observed that the inclusion of alfalfa hay led to a discernible alteration in the developmental trajectory of the rumen. Notably, there was a favorable shift in the rumen's volume, morphology, and the development of rumen papillae. Furthermore, ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation, collectively provide compelling evidence supporting the capacity of alfalfa hay to enhance rumen development and health through ruminal micrbiota-host crosstalks. Our findings elucidate the functional response of the rumen to alfalfa hay introduction, providing new insights into strategies for promoting healthy development of the rumen in young ruminants.
Topics: Sheep; Animals; Medicago sativa; RNA, Ribosomal, 16S; Rumen; Animal Feed; Fatty Acids, Volatile; Sheep, Domestic; Ruminants; Microbiota; Weight Gain
PubMed: 38179946
DOI: 10.1128/msystems.01034-23 -
Asian-Australasian Journal of Animal... Sep 2017The effect of flavonoids from alfalfa on the microbial flora was determined using molecular techniques of 16S ribosome deoxyribonucleic acid (rDNA) analysis.
OBJECTIVE
The effect of flavonoids from alfalfa on the microbial flora was determined using molecular techniques of 16S ribosome deoxyribonucleic acid (rDNA) analysis.
METHODS
Four primiparous Holstein heifers fitted with ruminal cannulas were used in a 4×4 Latin square design and fed a total mixed ration to which alfalfa flavonoids extract (AFE) was added at the rates of 0 (A, control), 20 (B), 60 (C), or 100 (D) mg per kg of heifer BW.
RESULTS
The number of operational taxonomic units in heifers given higher levels of flavonoid extract (C and D) was higher than for the two other treatments. The Shannon, Ace, and Chao indices for treatment C were significantly higher than for the other treatments (p<0.05). The number of phyla and genera increased linearly with increasing dietary supplementation of AFE (p<0.05). The principal co-ordinates analysis plot showed substantial differences in the microbial flora for the four treatments. The microbial flora in treatment A was similar to that in B, C, and D were similar by the weighted analysis. The richness of at the phylum level tended to increase with increasing AFE (p = 0.10). The proportion of at the phylum level increased linearly, whereas the proportion of decreased linearly with increasing AFE supplementation (p = 0.04). The percentage of , , and at the genus level decreased linearly with increasing AFE (p<0.05). The abundance of , , and at the genus level tended to decrease linearly with increasing AFE (0.05
CONCLUSION
Including AFE in the diet of dairy cows may alter the microbial composition of the rumen; however its effect on nutrient digestibility remains to be determined.
PubMed: 28183168
DOI: 10.5713/ajas.16.0839