Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake

Noel, Samantha Joan; Olijhoek, D.W.; Mclean, Farran; Løvendahl, Peter; Lund, Peter; Højberg, Ole

doi:10.3390/ani9080498

Cited by 53 publications

(49 citation statements)

References 43 publications

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“…On bacterial family level, 71% changed in relative abundances with HC feeding. The highest abundant families found, do overlap with other studies investigating fecal microbiota in cattle [ 35 ] and sheep [ 36 ]. However, some studies, as [ 9 ], found almost 42% Peptostreptococcaceae in the rectum of cattle, followed by Turicibacter , and Clostridium , and [ 29 ] mainly Planococaceae , Enterobacteriaceae , Moraxellaceae , Peptostreptococcaceae , and Erysipelotrichaceae , which were all below 1% abundance or not present in our study.…”

Section: Discussionsupporting

confidence: 80%

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations

Neubauer

Petri

Humer

et al. 2020

Animals

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Starch-rich diets can cause subacute ruminal acidosis (SARA) in dairy cows with potentially different susceptibility according to lactation number. We wanted to evaluate the bacterial community and the fermentation end products in feces to study susceptibility to hindgut acidosis and dysbiosis. Sixteen dairy cows received a medium-concentrate diet (MC, 40% concentrate, 18.8% starch) for one week and a high-concentrate diet (HC, 60% concentrate, 27.7% starch, DM) for four weeks. Milk yield, dry-matter intake, chewing activity, ruminal pH, milk constituents, and fecal samples for short-chain fatty acids (SCFA), pH, and 16S rRNA-gene sequencing were investigated. The HC feeding caused a reduction in fecal pH, bacterial diversity and richness, an increase in total SCFA, and a separate phylogenetic clustering of MC and HC samples. Ruminal and fecal pH had fair correlation (r = 0.5). Cows in the second lactation (2ndL) had lower dry matter intake (DMI) than cows of third or fourth or more lactations (3rdL; ≥4 L), whereas DMI/kg body weight was lower for ≥4 L than for 2ndL and 3rdL cows. The mean ruminal pH was highest in ≥4 L, whereas the time spent below the SARA threshold was highest for 3rdL cows. The latter also had higher total SCFA in the feces. Our results suggest that hindgut dysbiosis is caused by increased substrate flow to the hindgut, but further investigations are needed to define hindgut acidosis. The 3rdL cows were most susceptible to rumen acidosis and hindgut dysbiosis due to high DMI level, but missing counter regulations, as suggested happening in 2ndL and ≥4 L cows.

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Section: Discussionsupporting

confidence: 80%

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations

Neubauer

Petri

Humer

et al. 2020

Animals

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“…Alternatives, such as the use of oral samples as a proxy for the rumen microbiome, have been proposed [10] and shown to be good predictors for the bacteria community, but not for archaea. Other sampling alternatives for monitoring the GIT microbiome, such as colon/fecal are poorly investigated or limited to a small number of animals [11], despite being identified as crucial in other mammals [12][13][14].…”

Section: (Continued From Previous Page)mentioning

confidence: 99%

The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

Andrade

Bressani

Cuadrat

et al. 2020

J Animal Sci Biotechnol

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Background: The success of different species of ruminants in the colonization of a diverse range of environments is due to their ability to digest and absorb nutrients from cellulose, a complex polysaccharide found in leaves and grass. Ruminants rely on a complex and diverse microbial community, or microbiota, in a unique compartment known as the rumen to break down this polysaccharide. Changes in microbial populations of the rumen can affect the host's development, health, and productivity. However, accessing the rumen is stressful for the animal. Therefore, the development and use of alternative sampling methods are needed if this technique is to be routinely used in cattle breeding. To this end, we tested if the fecal microbiome could be used as a proxy for the rumen microbiome due to its accessibility. We investigated the taxonomic composition, diversity and interrelations of two different GIT compartments, rumen and feces, of 26 Nelore (Bos indicus) bulls, using Next Generation Sequencing (NGS) metabarcoding of bacteria, archaea and ciliate protozoa. Results: We identified 4265 Amplicon Sequence Variants (ASVs) from bacteria, 571 from archaea, and 107 from protozoa, of which 143 (96 bacteria and 47 archaea) were found common between both microbiomes. The most prominent bacterial phyla identified were Bacteroidetes (41.48%) and Firmicutes (56.86%) in the ruminal and fecal microbiomes, respectively, with Prevotella and Ruminococcaceae UCG-005 the most relatively abundant genera identified in each microbiome. The most abundant archaeal phylum identified was Euryarchaeota, of which Methanobrevibacter gottschalkii, a methanogen, was the prevalent archaeal species identified in both microbiomes. Protozoa were found exclusively identified in the rumen with Bozasella/ Triplumaria being the most frequent genus identified. Co-occurrence among ruminal and fecal ASVs reinforces the relationship of microorganisms within a biological niche. Furthermore, the co-occurrence of shared archaeal ASVs between microbiomes indicates a dependency of the predominant fecal methanogen population on the rumen population.

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“…3D, E). These indicate that microbiota structures closely related to the breeding environment, feeding method, and management measures (Crippen et al, 2019;Li et al, 2019;Noel et al, 2019). There were 626 (PC) and 649 (GC) OTUs shared among PC and GC groups, representing 26.6% and 24.4% of total reads separately in PC and GC environments, respectively.…”

Section: Analysis Of Microbiota Structurementioning

confidence: 81%

Comparing environmental microbiota of different growth stages of fresh water turtle Chinemys reevesii in pond and greenhouse cultivation

Zhou¹,

Xie²,

Sun³

et al. 2020

Preprint

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The microbial community structure is an important indicator for evaluating the water quality of the aquaculture environment. In this study, V4 regions of 16S rRNA gene of pond (PC) and greenhouse cultured (GC) C. reevesii were sequenced. Results showed that a total of 1,993,090 high quality counts and 105,159 observed OUTs were obtained; and the Chao1 richness estimator of PC was significantly higher than that of GC groups. Beta-diversity showed that the microbiota of two groups were isolated from each other. In addition, the correlation analysis of environmental factors showed that NO2-N, PH, PO4-P, and stocking density played significant roles in the bacterial community composition. The dominant phyla in PC groups were cyanobacteria, proteobacteria, actinobacteria, bacteroidetes, verrucomicrobia, planctomycetes; and in GC groups were proteobacteria, bacteroidetes, firmicutes, cyanobacteria, chloroﬂexi, actinobacteria. The functional prediction showed that the top5 Picrust prediction gene functions were protein processing in endoplasmic reticulum, retinol metabolism, proteasome, glycan binding proteins, and stilbenoid, diarylheptanoid and gingerol biosynthesis. Meanwhile, the numbers and types of KEGG pathway annotations showed a significant difference between the two cultivation environments. The prediction of bacterial phenotype implied that the GC environment is more likely to deteriorate, and turtles are more susceptible to pathogens than those of PC environment. This is the first report to explore and understand the difference of microbiota characteristics between different cultivation environments in different growth stages of C. reevesii, which will provide basic data for water quality adjustment, disease prevention, and healthy breeding of turtle.

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Rumen and Fecal Microbial Community Structure of Holstein and Jersey Dairy Cows as Affected by Breed, Diet, and Residual Feed Intake

Cited by 53 publications

References 43 publications

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations

The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen

Comparing environmental microbiota of different growth stages of fresh water turtle Chinemys reevesii in pond and greenhouse cultivation

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