scholarly journals Comparison of rumen microbe taxa among wild and domestic ruminants

2015 ◽  
Author(s):  
◽  
Tasia Marie Taxis
Keyword(s):  
Microbial Community ◽  
Host Species ◽  
Plant Material ◽  
Rumen Content ◽  
Phenotypic Traits ◽  
Host Animal ◽  
Domestic Ruminants ◽  
Host Diet ◽  
Rumen Microbe ◽  
On Farm

Microbes that inhabit the rumen provide a diverse set of enzymes that degrade ingested plant material. Without microbes, ruminants could not survive. Our research has focused on identifying microbial taxa associated with environment and phenotypic traits of host animals in order to improve livestock production and efficiency. Rumen contents were collected from a total of 48 animals from five host species, both wild and domestic, consuming either a concentrate- or forage-based diet. The objectives of this study were to analyze the distribution of microbial taxa among host species and identify microbial taxa associated with host diet, species, and domestication status. DNA was extracted from rumen content and sequenced for identification of microbial taxa present within each host animal. The distribution of microbial taxa was similar among host species. Each host species contained a few highly abundant microbial taxa and many microbial taxa in lower abundance. As host species were added to the analysis, the total number of microbial taxa identified increased and the number of microbial taxa common among all host species decreased, supporting the existence of a core microbial community. In this study we identified 66, 73, and 23 microbial taxa that differed among host diet, species, and domestication status, respectively. While on farm implications are far from being offered, studies of the microbial community add to the breadth of knowledge and identify microbes associated with performance and efficiency of livestock.

scholarly journals Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets

2021 ◽  
Vol 12 ◽  
Author(s):  
Chiron J. Anderson ◽  
Lucas R. Koester ◽  
Stephan Schmitz-Esser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Species ◽  
De Novo ◽  
Management Practice ◽  
Meta Analysis ◽  
Illumina Miseq ◽  
Rumen Content ◽  
Rrna Gene ◽  
The Core

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

scholarly journals Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

2012 ◽  
Vol 78 (20) ◽  
pp. 7327-7336 ◽  
Author(s):  
James Angus Chandler ◽  
Jonathan A. Eisen ◽  
Artyom Kopp
Keyword(s):  
Host Species ◽  
Bacterial Communities ◽  
Sampling Strategy ◽  
Holistic Approach ◽  
Content Type ◽  
Yeast Community ◽  
Comprehensive Picture ◽  
Host Diet ◽  
Host Microbe Interactions ◽  
Future Work

ABSTRACTThe combination of ecological diversity with genetic and experimental tractability makesDrosophilaa powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts inDrosophilaphysiology, behavior, and fitness, most recent work has focused onDrosophila-bacterial interactions. In order to get a more complete understanding of theDrosophilamicrobiome, we characterized the yeast communities associated with differentDrosophilaspecies collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of theDrosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed inDrosophilabacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach.

scholarly journals Inactivation of Enterohemorrhagic Escherichia coli in Rumen Content- or Feces-Contaminated Drinking Water for Cattle

2006 ◽  
Vol 72 (5) ◽  
pp. 3268-3273 ◽  
Author(s):  
Tong Zhao ◽  
Ping Zhao ◽  
Joe W. West ◽  
John K. Bernard ◽  
Heath G. Cross ◽  
...  
Keyword(s):  
Drinking Water ◽  
Lactic Acid ◽  
Chlorine Dioxide ◽  
Caprylic Acid ◽  
Acid Treatment ◽  
Calcium Sulfate ◽  
Rumen Content ◽  
E Coli ◽  
Water Treatments ◽  
On Farm

ABSTRACT Cattle drinking water is a source of on-farm Escherichia coli O157:H7 transmission. The antimicrobial activities of disinfectants to control E. coli O157:H7 in on-farm drinking water are frequently neutralized by the presence of rumen content and manure that generally contaminate the drinking water. Different chemical treatments, including lactic acid, acidic calcium sulfate, chlorine, chlorine dioxide, hydrogen peroxide, caprylic acid, ozone, butyric acid, sodium benzoate, and competing E. coli, were tested individually or in combination for inactivation of E. coli O157:H7 in the presence of rumen content. Chlorine (5 ppm), ozone (22 to 24 ppm at 5�C), and competing E. coli treatment of water had minimal effects (<1 log CFU/ml reduction) on killing E. coli O157:H7 in the presence of rumen content at water-to-rumen content ratios of 50:1 (vol/wt) and lower. Four chemical-treatment combinations, including (i) 0.1% lactic acid, 0.9% acidic calcium sulfate, and 0.05% caprylic acid (treatment A); (ii) 0.1% lactic acid, 0.9% acidic calcium sulfate, and 0.1% sodium benzoate (treatment B); (iii) 0.1% lactic acid, 0.9% acidic calcium sulfate, and 0.5% butyric acid (treatment C); and (iv) 0.1% lactic acid, 0.9% acidic calcium sulfate, and 100 ppm chlorine dioxide (treatment D); were highly effective (>3 log CFU/ml reduction) at 21�C in killing E. coli O157:H7, O26:H11, and O111:NM in water heavily contaminated with rumen content (10:1 water/rumen content ratio [vol/wt]) or feces (20:1 water/feces ratio [vol/wt]). Among them, treatments A, B, and C killed >5 log CFU E. coli O157:H7, O26:H11, and O111:NM/ml within 30 min in water containing rumen content or feces, whereas treatment D inactivated approximately 3 to 4 log CFU/ml under the same conditions. Cattle given water containing treatment A or C or untreated water (control) ad libitum for two 7-day periods drank 15.2, 13.8, and 30.3 liters/day, respectively, and cattle given water containing 0.1% lactic acid plus 0.9% acidic calcium sulfate (pH 2.1) drank 18.6 liters/day. The amounts of water consumed for all water treatments were significantly different from that for the control, but there were no significant differences among the water treatments. Such treatments may best be applied periodically to drinking water troughs and then flushed, rather than being added continuously, to avoid reduced water consumption by cattle.

scholarly journals How parasitoid females produce sexy sons: a causal link between oviposition preference, dietary lipids and mate choice in Nasonia

2011 ◽  
Vol 278 (1722) ◽  
pp. 3286-3293 ◽  
Author(s):  
Birgit Blaul ◽  
Joachim Ruther
Keyword(s):  
Parasitic Wasp ◽  
Oviposition Preference ◽  
Causal Link ◽  
Dietary Lipids ◽  
Phenotypic Traits ◽  
Causal Connection ◽  
Host Diet ◽  
Sexual Selection Theory ◽  
The Right

Sexual selection theory predicts that phenotypic traits used to choose a mate should reflect honestly the quality of the sender and thus, are often costly. Physiological costs arise if a signal depends on limited nutritional resources. Hence, the nutritional condition of an organism should determine both its quality as a potential mate and its ability to advertise this quality to the choosing sex. In insects, the quality of the offspring's nutrition is often determined by the ovipositing female. A causal connection, however, between the oviposition decisions of the mother and the mating chances of her offspring has never been shown. Here, we demonstrate that females of the parasitic wasp Nasonia vitripennis prefer those hosts for oviposition that have been experimentally enriched in linoleic acid (LA). We show by 13 C-labelling that LA from the host diet is a precursor of the male sex pheromone. Consequently, males from LA-rich hosts produce and release higher amounts of the pheromone and attract more virgin females than males from LA-poor hosts. Finally, males from LA-rich hosts possess three times as many spermatozoa as those from LA-poor hosts. Hence, females making the right oviposition decisions may increase both the fertility and the sexual attractiveness of their sons.

scholarly journals Evaluation of on-farm indicators of gilt reproductive performance potential at 21 days of age1

2020 ◽  
Vol 4 (4) ◽  
Author(s):  
Kayla M Mills ◽  
Allan P Schinckel ◽  
Jebadiah G Stevens ◽  
Theresa M Casey ◽  
Kara R Stewart
Keyword(s):  
Reproductive Performance ◽  
Average Daily Gain ◽  
Low Fertility ◽  
Phenotypic Traits ◽  
High Fertility ◽  
Swine Production ◽  
Performance Potential ◽  
Selection Decisions ◽  
Binomial Regression ◽  
On Farm

Abstract Selection of replacements for the sow herd is one of the most important facets in swine production. Although our current methods of selection are effective, there is still a large amount of variation in sow reproductive performance traits such as pigs per sow per year (PSY). Therefore, the objective of this study was to determine if on-farm phenotypic traits at 21 d postnatal (PN) or perinatal environmental factors could predict sow reproductive performance. Data were prospectively collected from 2,146 gilts born on a commercial sow production facility and included birth and weaning weights, vulva length and width at 21 d PN, birth and nursing litter size, days nursed, average daily gain from birth to weaning, and age at first estrus. Of the initial animals, 400 (17%) were selected for the sow herd, 353 remained after removal of animals culled for non-reproductive reasons. Animals were assigned to 1 of 5 reproductive performance categories based on observation of estrus or pigs per sow per year (PSY) across two farrowings: High Fertility (HF; 23%; n = 82; ≥26 PSY), Middle Fertility (MF2; 12%; n = 43; 20–25 PSY), Low Fertility (MF3; 15%; n = 54; &lt;20 PSY), Infertile-Estrus (IFe; 10%; n = 36; estrus, no pregnancy), and Infertile-No Estrus (IFno; 39%; n = 138; no estrus, no pregnancy). Generalized linear model analysis indicated vulva width (P = 0.03) was related to PSY, however, it only explained 1.5% of the total variation in PSY. To determine if preweaning variables were predictive of gilt fertility outcome, animals were grouped as those that became pregnant (n = 179) or not (n = 174). Vulva width tended to be greater in fertile animals versus infertile (P = 0.07). Binomial regression analysis revealed a positive relationship between vulva width and gilt fertility, however, this relationship is not strong enough to make sow herd selection decisions.

scholarly journals The Effects of Artificially Dosed Adult Rumen Contents on Abomasum Transcriptome and Associated Microbial Community Structure in Calves

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 424
Author(s):  
Naren Gaowa ◽  
Wenli Li ◽  
Brianna Murphy ◽  
Madison Cox
Keyword(s):  
Community Structure ◽  
Immune System ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Molecular Mechanisms ◽  
High Efficiency ◽  
Rumen Content ◽  
System Process ◽  
Significant Difference ◽  
Immune System Process

This study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), n = 4), or sterilized rumen content (Con, n = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing. Abomasum tissues were collected immediately after sacrifice at 8 weeks of age. Five genera (Tannerella, Desulfovibrio, Deinococcus, Leptotrichia, and Eubacterium; P < 0.05) showed significant difference in abundance between the treatments. A total of 975 differentially expressed genes were identified (P < 0.05, fold-change > 1.5, mean read-counts > 5). Pathway analysis indicated that up-regulated genes were involved in immune system process and defense response to virus, while the down-regulated genes involved in ion transport, ATP biosynthetic process, and mitochondrial electron transport. Positive correlation (r > 0.7, P < 0.05) was observed between TRPM4 gene and Desulfovibrio, which was significantly higher in the HE group. TRPM4 had a reported role in the immune system process. In conclusion, the dosing of adult rumen contents to calves can alter not only the composition of active microorganisms in the abomasum but also the molecular mechanisms in the abomasum tissue, including reduced protease secretion and decreased hydrochloric acid secretion.

scholarly journals Susceptibility across host species is independent of dietary protein to carbohydrate ratios

2020 ◽  
Author(s):  
Katherine E Roberts ◽  
Ben Longdon
Keyword(s):  
Viral Load ◽  
Dietary Protein ◽  
Host Species ◽  
Rna Virus ◽  
Ecological Factors ◽  
Host Shift ◽  
Host Susceptibility ◽  
Novel Host ◽  
Host Diet ◽  
Host Parasite

AbstractThe likelihood of a successful host shift of a parasite to a novel host species can be influenced by environmental factors that can act on both the host and parasite. Changes in nutritional resource availability have been shown to alter pathogen susceptibility and the outcome of infection in a range of systems. Here we examined how dietary protein to carbohydrate altered susceptibility in a large cross infection experiment. We infected 27 species of Drosophilidae with an RNA virus on three food types of differing protein to carbohydrate ratios. We then measured how viral load and mortality across species was affected by changes in diet. We found that changes in the protein:carbohydrate in the diet did not alter the outcomes of infection, with strong positive inter-species correlations in both viral load and mortality across diets, suggesting no species by diet interaction. Mortality and viral load were strongly positively correlated, and this association was consistent across diets. This suggests changes in diet may give consistent outcomes across host species, and may not be universally important in determining host susceptibility to pathogens.Impact StatementA successful host shift of a parasite from one susceptible species to a novel host can be influenced by many ecological factors. Changes in host diet can alter the immune response and outcomes of host–parasite interactions and could potentially alter the outcome of a virus host shift. To investigate, we infected 27 species of Drosophilidae with an RNA virus (DCV) across three food types with differing protein to carbohydrate ratios. We then looked at pathogen loads and survival of infected hosts compared to uninfected controls. Changes in the ratio of protein to carbohydrate did not alter susceptibility to DCV across host species.

scholarly journals Characterizing the Alteration in Rumen Microbiome and Carbohydrate-Active Enzymes Profile with Forage of Muskoxen Rumen through Comparative Metatranscriptomics

2021 ◽  
Vol 10 (1) ◽  
pp. 71
Author(s):  
Xiaofeng Wu ◽  
Chijioke O. Elekwachi ◽  
Shiping Bai ◽  
Yuheng Luo ◽  
Keying Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Plant Biomass ◽  
High Arctic ◽  
Glycoside Hydrolases ◽  
Microbial Consortia ◽  
Biomass Hydrolysis ◽  
Host Animal ◽  
Ovibos Moschatus ◽  
Plant Polysaccharide ◽  
Rumen Microbiome

Muskox (Ovibos moschatus), as the biggest herbivore in the High Arctic, has been enduring the austere arctic nutritional conditions and has evolved to ingest and digest scarce and high lignified forages to support the growth and reproduce, implying probably harbor a distinct microbial reservoir for the deconstruction of plant biomass. Therefore, metagenomics approach was applied to characterize the rumen microbial community and understand the alteration in rumen microbiome of muskoxen fed either triticale straw or brome hay. The difference in the structure of microbial communities including bacteria, archaea, fungi, and protozoa between the two forages was observed at the taxonomic level of genus. Further, although the highly abundant phylotypes in muskoxen rumen fed either triticale straw or brome hay were almost the same, the selective enrichment different phylotypes for fiber degrading, soluble substrates fermenting, electron and hydrogen scavenging through methanogenesis, acetogenesis, propionogenesis, and sulfur-reducing was also noticed. Specifically, triticale straw with higher content of fiber, cellulose selectively enriched more lignocellulolytic taxa and electron transferring taxa, while brome hay with higher nitrogen content selectively enriched more families and genera for degradable substrates-digesting. Intriguingly, the carbohydrate-active enzyme profile suggested an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on triticale straw. The majority of the cellulases belonged to fiver GH families (i.e., GH5, GH6, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus, Piromyces, Neocallimastix, and Fibrobacter. Abundance of major genes coding for hemicellulose digestion was higher than cellulose mainly including GH8, GH10, GH16, GH26, and GH30, and these enzymes were produced by members of the genera Fibrobacter, Ruminococcus, and Clostridium. Oligosaccharides were mainly of the GH1, GH2, GH3, and GH31 types and were associated with the genera Prevotella and Piromyces. Our results strengthen metatranscriptomic evidence in support of the understanding of the microbial community and plant polysaccharide response to changes in the feed type and host animal. The study also establishes these specific microbial consortia procured from triticale straw group can be used further for efficient plant biomass hydrolysis.

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