scholarly journals A pioneer calf foetus microbiome

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Cesar E. Guzman ◽  
Jennifer L. Wood ◽  
Eleonora Egidi ◽  
Alison C. White-Monsant ◽  
Lucie Semenec ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Amniotic Fluid ◽  
Direct Evidence ◽  
Ruminal Fluid ◽  
Bacterial Phyla ◽  
Sample Contamination ◽  
Bacterial And Archaeal Communities ◽  
Viable Bacteria ◽  
Archaeal Communities

Abstract Foetus sterility until parturition is under debate due to reports of microorganisms in the foetal environment and meconium. Sufficient controls to overcome sample contamination and provide direct evidence of microorganism viability in the pre-rectal gastrointestinal tract (GIT) have been lacking. We conducted molecular and culture-based analyses to investigate the presence of a microbiome in the foetal GIT of calves at 5, 6 and 7 months gestation, while controlling for contamination. The 5 components of the GIT (ruminal fluid, ruminal tissue, caecal fluid, caecal tissue and meconium) and amniotic fluid were found to contain a pioneer microbiome of distinct bacterial and archaeal communities. Bacterial and archaeal richness varied between GIT components. The dominant bacterial phyla in amniotic fluid differed to those in ruminal and caecal fluids and meconium. The lowest bacterial and archaeal abundances were associated with ruminal tissues. Viable bacteria unique to the ruminal fluids, which were not found in the controls from 5, 6 and 7 months gestation, were cultured, subcultured, sequenced and identified. We report that the foetal GIT is not sterile but is spatially colonised before birth by a pioneer microbiome.

scholarly journals Stability Assessment of the Rumen Bacterial and Archaeal Communities in Dairy Cows Within a Single Lactation and Its Association With Host Phenotype

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhigang Zhu ◽  
Gareth Frank Difford ◽  
Samantha Joan Noel ◽  
Jan Lassen ◽  
Peter Løvendahl ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Dairy Cows ◽  
The Other ◽  
Lactation Period ◽  
Stability Assessment ◽  
Value Analysis ◽  
Bacterial Phyla ◽  
Other Hand ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Better characterization of changes in the rumen microbiota in dairy cows over the lactation period is crucial for understanding how microbial factors may potentially be interacting with host phenotypes. In the present study, we characterized the rumen bacterial and archaeal community composition of 60 lactating Holstein dairy cows (33 multiparous and 27 primiparous), sampled twice within the same lactation with a 122 days interval. Firmicutes and Bacteroidetes dominated the rumen bacterial community and showed no difference in relative abundance between samplings. Two less abundant bacterial phyla (SR1 and Proteobacteria) and an archaeal order (Methanosarcinales), on the other hand, decreased significantly from the mid-lactation to the late-lactation period. Moreover, between-sampling stability assessment of individual operational taxonomic units (OTUs), evaluated by concordance correlation coefficient (C-value) analysis, revealed the majority of the bacterial OTUs (6,187 out of 6,363) and all the 79 archaeal OTUs to be unstable over the investigated lactation period. The remaining 176 stable bacterial OTUs were mainly assigned to Prevotella, unclassified Prevotellaceae, and unclassified Bacteroidales. Milk phenotype-based screening analysis detected 32 bacterial OTUs, mainly assigned to unclassified Bacteroidetes and Lachnospiraceae, associated with milk fat percentage, and 6 OTUs, assigned to Ruminococcus and unclassified Ruminococcaceae, associated with milk protein percentage. These OTUs were only observed in the multiparous cows. None of the archaeal OTUs was observed to be associated with the investigated phenotypic parameters, including methane production. Co-occurrence analysis of the rumen bacterial and archaeal communities revealed Fibrobacter to be positively correlated with the archaeal genus vadinCA11 (Pearson r = 0.76) and unclassified Methanomassiliicoccaceae (Pearson r = 0.64); vadinCA11, on the other hand, was negatively correlated with Methanobrevibacter (Pearson r = –0.56). In conclusion, the rumen bacterial and archaeal communities of dairy cows displayed distinct stability at different taxonomic levels. Moreover, specific members of the rumen bacterial community were observed to be associated with milk phenotype parameters, however, only in multiparous cows, indicating that dairy cow parity could be one of the driving factors for host–microbe interactions.

PSII-B-28 Investigation of the presence of bacterial microbiota in 12-week-old bovine fetuses

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 352-352
Author(s):  
Samat Amat ◽  
Devin B Holman ◽  
Kaycie Schmidt ◽  
kacie L L McCarthy ◽  
Sheri T T Dorsam ◽  
...  
Keyword(s):  
Microbial Community ◽  
Amniotic Fluid ◽  
Shannon Index ◽  
Rrna Gene ◽  
Sample Type ◽  
Microscopy Imaging ◽  
Tissue Samples ◽  
Early Gestation ◽  
Bacterial Phyla ◽  
Bovine Fetuses

Abstract A recent study reported the existence of a diverse microbiota in 5-to-7-month-old calf fetuses, suggesting that colonization of the bovine gut with so-called “pioneer” microbiota may begin during mid-gestation. In the present study, we investigated the microbiota in bovine fetuses at early gestation. Amniotic and allantoic fluids, and intestinal and placental (cotyledon) tissue samples harvested from fetuses (n = 33) on day 83 of gestation were processed for the assessment of fetal microbiota using 16S rRNA gene sequencing. The sequencing results revealed that a diverse and complex microbial community was present in allantoic and amniotic fluids, and fetal intestine and placenta on day 83 of gestation in beef cattle. Microbial community structure was significantly different between allantoic and amniotic fluid, and intestinal and placental microbiota (0.047 ≥ R2 ≥ 0.019, P ≤ 0.031). Allantoic fluid had a greater (P < 0.05) microbial richness (number of OTUs) (122 ± 10) compared to amniotic fluid (84 ± 6), intestine (63 ± 7) and placenta (66 ± 6). Microbial diversity (Shannon index) was similar for the intestinal and placental samples, and both were less diverse compared to the fetal fluid microbiota (P < 0.05). At the phylum level, 39 different archaeal and bacterial phyla were detected across all fetal samples, with Proteobacteria (55%), Firmicutes (16.2%), Actinobacteria (13.6%) and Bacteroidetes (5%) predominating. Among the 20 most relatively abundant bacterial genera, Acidovorax, Acinetobacter, Brucella, Corynebacterium, Enterococcus, Exiguobacterium and Stenotrophomonas differed by fetal sample type (P < 0.05). A total of 55 taxa were shared among the four different microbial communities. qPCR of bacteria in the intestine and placenta samples as well as scanning electron microscopy imaging of fetal fluids provided additional evidence for the presence of a microbiota in these samples. Overall, the results of this study indicate that colonization with pioneer microbiota may occur during early gestation in bovine fetuses.

scholarly journals Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Forests ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 550 ◽  
Author(s):  
Huili Feng ◽  
Jiahuan Guo ◽  
Weifeng Wang ◽  
Xinzhang Song ◽  
Shuiqiang Yu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Rrna Gene ◽  
Poplar Plantation ◽  
Plantation Forest ◽  
Bacterial And Archaeal Communities ◽  
Different Depths ◽  
Archaeal Communities

Understanding the composition and diversity of soil microorganisms that typically mediate the soil biogeochemical cycle is crucial for estimating greenhouse gas flux and mitigating global changes in plantation forests. Therefore, the objectives of this study were to investigate changes in diversity and relative abundance of bacteria and archaea with soil profiles and the potential factors influencing the vertical differentiation of microbial communities in a poplar plantation. We investigated soil bacterial and archaeal community compositions and diversities by 16S rRNA gene Illumina MiSeq sequencing at different depths of a poplar plantation forest in Chenwei forest farm, Sihong County, Jiangsu, China. More than 882,422 quality-filtered 16S rRNA gene sequences were obtained from 15 samples, corresponding to 34 classified phyla and 68 known classes. Ten major bacterial phyla and two archaeal phyla were found. The diversity of bacterial and archaeal communities decreased with depth of the plantation soil. Analysis of variance (ANOVA) of relative abundance of microbial communities exhibited that Nitrospirae, Verrucomicrobia, Latescibacteria, GAL15, SBR1093, and Euryarchaeota had significant differences at different depths. The transition zone of the community composition between the surface and subsurface occurred at 10–20 cm. Overall, our findings highlighted the importance of depth with regard to the complexity and diversity of microbial community composition in plantation forest soils.

114 Alterations of the rumen bacterial and archaeal communities in growing and finishing beef cattle and its effects on methane emissions

2016 ◽  
Vol 94 (suppl_2) ◽  
pp. 53-54 ◽  
Author(s):  
A. L. Knoell ◽  
C. L. Anderson ◽  
A. C. Pesta ◽  
G. E. Erickson ◽  
T. J. Klopfenstein ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Methane Emissions ◽  
Bacterial And Archaeal Communities ◽  
Finishing Beef Cattle ◽  
Archaeal Communities

scholarly journals Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

2010 ◽  
Vol 5 (3) ◽  
pp. 389-402 ◽  
Author(s):  
Frank Rasche ◽  
Daniela Knapp ◽  
Christina Kaiser ◽  
Marianne Koranda ◽  
Barbara Kitzler ◽  
...  
Keyword(s):  
Resource Availability ◽  
Beech Forest ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities
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