Feed Additives Differentially Impact the Epimural Microbiota and Host Epithelial Gene Expression of the Bovine Rumen Fed Diets Rich in Concentrates

Petri, Renée M.; Neubauer, Viktoria; Humer, Elke; Kröger, Iris; Reisinger, Nicole; Zebeli, Qendrim

doi:10.3389/fmicb.2020.00119

Cited by 26 publications

(30 citation statements)

References 55 publications

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“…These included projects conducted in Austria [9,10,[17][18][19][20], the USA [21,22], Ireland (unpublished; PRJNA484585), Belgium [23], and Germany [24]. Studies conducted in Austria [9,10], [17][18][19][20] were all conducted at the same farm and in some cases using the same animals. Two studies conducted in the USA were conducted in different farms [21,22].…”

Section: Datasetsmentioning

confidence: 99%

“…All projects included purebred Holstein-Friesian dairy cows, with the exception of the study from Ireland which used Holstein and Charolais steers (unpublished; PRJNA484585). Biopsy samples were collected from several locations: ventral sac [9,10,[17][18][19][20][21]23,24], (unpublished; PRJNA484585), dorsal sac [22], cranial sac [21], caudoventral blind sac [21], and caudodorsal blind sac [21]. All studies used primers sets for Illumina paired-end sequencing of the V4 [21,22,24], V3-4 [23], and V3-5 [9,10,[17][18][19][20] hypervariable regions (Table 2).…”

Section: Datasetsmentioning

confidence: 99%

“…Biopsy samples were collected from several locations: ventral sac [9,10,[17][18][19][20][21]23,24], (unpublished; PRJNA484585), dorsal sac [22], cranial sac [21], caudoventral blind sac [21], and caudodorsal blind sac [21]. All studies used primers sets for Illumina paired-end sequencing of the V4 [21,22,24], V3-4 [23], and V3-5 [9,10,[17][18][19][20] hypervariable regions (Table 2). Different DNA extraction methods were used, either based on kits [9,10], [17][18][19][20]22,24] or phenol-chloroform extraction methods [21,23], with [9,10,[17][18][19][20][21][22][23] or without bead beating [24].…”

Section: Datasetsmentioning

confidence: 99%

“…All studies used primers sets for Illumina paired-end sequencing of the V4 [21,22,24], V3-4 [23], and V3-5 [9,10,[17][18][19][20] hypervariable regions (Table 2). Different DNA extraction methods were used, either based on kits [9,10], [17][18][19][20]22,24] or phenol-chloroform extraction methods [21,23], with [9,10,[17][18][19][20][21][22][23] or without bead beating [24]. None of the studies reported the inclusion of positive controls e.g., a mock community or an extraction/reagent (negative) control.…”

Section: Datasetsmentioning

confidence: 99%

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Unveiling the Bovine Epimural Microbiota Composition and Putative Function

et al. 2021

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Numerous studies have used the 16S rRNA gene target in an attempt to characterize the structure and composition of the epimural microbiota in cattle. However, comparisons between studies are challenging, as the results show large variations associated with experimental protocols and bioinformatics methodologies. Here, we present a meta-analysis of the rumen epimural microbiota from 11 publicly available amplicon studies to assess key technical and biological sources of variation between experiments. Using the QIIME2 pipeline, 332 rumen epithelial microbiota samples were analyzed to investigate community structure, composition, and functional potential. Despite having a significant impact on microbial abundance, country of origin, farm, hypervariable region, primer set, animal variability, and biopsy location did not obscure the identification of a core microbiota. The bacterial genera Campylobacter, Christensenellaceae R-7 group, Defluviitaleaceae UCG-011, Lachnospiraceae UCG-010, Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-014, Succiniclasticum, Desulfobulbus, and Comamonas spp. were found in nearly all epithelium samples (>90%). Predictive analysis (PICRUSt) was used to assess the potential functions of the epithelial microbiota. Regularized canonical correlation analysis identified several pathways associated with the biosynthesis of precursor metabolites in Campylobacter, Comamonas, Desulfobulbus, and Ruminococcaceae NK4A214, highlighting key metabolic functions of these microbes within the epithelium.

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Section: Datasetsmentioning

confidence: 99%

Section: Datasetsmentioning

confidence: 99%

Section: Datasetsmentioning

confidence: 99%

Section: Datasetsmentioning

confidence: 99%

See 2 more Smart Citations

Unveiling the Bovine Epimural Microbiota Composition and Putative Function

et al. 2021

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“…As mentioned above, diets with high energy and protein levels in Group H effectively promoted the growth performance and carcass characteristics of goats. Meanwhile, the digestion and absorption of these diets were closely related to the rumen bacteria [40][41][42]. A previous study reported that the changes in the ruminal microbiota could help promote the ADG of goats [5].…”

Section: Comparison Of the Composition And Differences Of Ruminal Bacmentioning

confidence: 98%

Dynamic alterations in rumen bacterial community and metabolome characteristics in response to feed nutrient levels of cashmere goats

Wang

Tang

Xiao

et al. 2020

Preprint

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Background: Dietary energy and protein play important roles in rumen fermentation. However, the comprehensive impacts of dietary energy and protein on rumen bacterial composition and ruminal metabolites were largely unknown. Therefore, the objective of the current study was to investigate the changes in rumen bacterial community and metabolites in response to the diets with simultaneous changes of dietary energy and protein levels in Shaanbei white cashmere goats (SWCG). Methods: A total of 12 ruminal samples were collected from SWCG, which were divided into two groups, including high-energy and high-protein (Group H; crude protein, CP: 9.37% in dry matter; metabolic energy, ME: 9.24 MJ/kg) or control (Group C; CP: 8.73%; ME:8.60 MJ/kg) groups. The experiment lasted for 65 days, including 10 days for adaptation. 16S rRNA gene sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to identify the rumen bacterial community. Metabolomics analysis was done to investigate the rumen metabolites and the related metabolic pathways in Groups C and H. Results: The study observed 539 genera belonging to 30 phyla, which were distributed throughout the rumen samples. The high-energy and high-protein diets increased the relative abundance of phylum Bacteroidetes and genera Prevotella_1 and Succiniclasticum, while decreased the number of phylum Proteobacteria (p<0.05). Among the 24 differential metabolites (VIP>1.0, p<0.05) detected in this study, the dominant differential metabolites were amino acids, peptides and analogs. Tyrosine metabolism played an important role among the 9 main metabolic pathways. Correlation analysis revealed that Prevotella_1 showed strong positive correlation with 5-methoxyindole-3-acetic acid (r=0.601, p<0.05) and catechol (r=0.608, p<0.05). Succiniclasticum was positively correlated with 2-ketoadipate (r=0.741, p<0.01). Conclusions: Our findings revealed that the diets with high energy and protein in Group H significantly altered the composition of ruminal bacteria and metabolites, which could help to improve the dietary energy and protein use efficiency in goats.

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Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria

Botero Rute,

Caro-Quintero,

Acosta-González

2023

Microb Ecol

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The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10−2, 10−6, 10−12), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10−2 and 10−6 dilutions clustered closely while the 10−12 dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.

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Feed Additives Differentially Impact the Epimural Microbiota and Host Epithelial Gene Expression of the Bovine Rumen Fed Diets Rich in Concentrates

Cited by 26 publications

References 55 publications

Unveiling the Bovine Epimural Microbiota Composition and Putative Function

Unveiling the Bovine Epimural Microbiota Composition and Putative Function

Dynamic alterations in rumen bacterial community and metabolome characteristics in response to feed nutrient levels of cashmere goats

Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria

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