Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations

Kumar, Himansu; Park, Woncheol; Srikanth, Krishnamoorthy; Choi, Bong-Hwan; Cho, Eun Seok; Lee, Kyung-Tai; Kim, Junmo; Kim, Kwangmin; Park, Jun Hyung; Lim, Dajeong

doi:10.3390/genes10050382

Cited by 14 publications

(11 citation statements)

References 81 publications

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“…LEfSe is a tool for the discovery of biomarker bacteria among various samples by analyzing the abundance of microbes [ 50 ]. We also implemented this tool to analyze the microbial biomarkers in our swine slurry data, and found that Clostridium and Lactobacillus were predominant across the samples and corroborated the earlier findings [ 51 ]. We reported the specific bacterial biomarkers in each week of storage period.…”

Section: Discussionsupporting

confidence: 83%

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Kumar

Jang

Kim³

et al. 2020

Animals

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Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson’s correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism’s metabolic activity and the microbes present in the gastro intestinal tract (GIT).

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Section: Discussionsupporting

confidence: 83%

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Kumar

Jang

Kim³

et al. 2020

Animals

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“…A similar study in sheep indicated that the abundance of microbial ABC transporters differed between Tibetan and Small Tail Han breeds grown under the same environmental conditions [41]. In addition, the metabolic pathways of carbohydrates (fructose, mannose, and galactose), amino acids (BCAAs, AAAs, and lysine), and lipids (glycerolipid) have been shown to differ among farm animal breeds grown under the standardized feeding conditions [6,[42][43][44][45]. The breed-associated KEGG pathways showed substantial overlap with the breed-associated KOs.…”

Section: Discussionmentioning

confidence: 94%

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

Zhou

Zhang

et al. 2021

BMC Vet Res

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Background Gut microbial compositional and functional variation can affect health and production performance of farm animals. Analysing metabolites in biological samples provides information on the basic mechanisms that affect the well-being and production traits in farm animals. However, the extent to which host breeds affect the gut microbiome and serum metabolome in meat rabbits is still unknown. In this study, the differences in phylogenetic composition and functional capacities of gut microbiota in two commercial rabbit breeds Elco and Ira were determined by 16S rRNA gene and metagenomic sequencing. The alternations in serum metabolome in the two rabbit breeds were detected using ultra-performance liquid chromatography system coupled with quadrupole time of flight mass spectrometry (UPLC-QTOFMS). Results Sequencing results revealed that there were significant differences in the gut microbiota of the two breeds studied, suggesting that host breeds affect structure and diversity of gut microbiota. Numerous breed-associated microorganisms were identified at different taxonomic levels and most microbial taxa belonged to the families Lachnospiraceae and Ruminococcaceae. In particular, several short-chain fatty acids (SCFAs) producing species including Coprococcus comes, Ruminococcus faecis, Ruminococcus callidus, and Lachnospiraceae bacterium NK4A136 could be considered as biomarkers for improving the health and production performance in meat rabbits. Additionally, gut microbial functional capacities related to bacterial chemotaxis, ABC transporters, and metabolism of different carbohydrates, amino acids, and lipids varied greatly between rabbit breeds. Several fatty acids, amino acids, and organic acids in the serum were identified as breed-associated, where certain metabolites could be regarded as biomarkers correlated with the well-being and production traits of meat rabbits. Correlation analysis between breed-associated microbial species and serum metabolites revealed significant co-variations, indicating the existence of cross-talk among host-gut microbiome-serum metabolome. Conclusions Our study provides insight into how gut microbiome and serum metabolome of meat rabbits are affected by host breeds and uncovers potential biomarkers important for breed improvement of meat rabbits.

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“…Consistent with a previous report (Yang et al 2018), the LRFI pigs tended to have higher α variety (Chao 1, Sob, Shannon, ACE, Coverage, and PD) than the HRFI pigs, albeit no significant difference in richness or evenness were found between the two groups. The composition of intestinal microorganisms can be influenced by diet, age, host genetics and environmental factors (Benson et al 2010;Buzoianu et al 2012;Kumar et al 2019). Previous studies indicated that there were significant differences in intestinal microbial composition among pigs at different grow stages (Ke et al 2019;Kumar et al 2019).…”

Section: Discussionmentioning

confidence: 99%

“…The composition of intestinal microorganisms can be influenced by diet, age, host genetics and environmental factors (Benson et al 2010;Buzoianu et al 2012;Kumar et al 2019). Previous studies indicated that there were significant differences in intestinal microbial composition among pigs at different grow stages (Ke et al 2019;Kumar et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing

Feng

Gao

et al. 2020

AMB Expr

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Improving the predication efficiency of porcine production performance at early stage will contribute to reducing the breeding and production costs. The intestinal microbiota had received plenty of attention in recent years due to their influence on host health and performance. The purpose of this study was to investigate the relationship between the fecal microbiota at early growth period and porcine feed efficiency (FE) under a commercial feeding environment. Ninety-one pigs were reordered according to the residual feed intake (RFI) values between day 90 on test and day 160 off test, 9 lowest RFI pigs and 9 highest RFI pigs were selected as the LRFI group and the HRFI group, respectively. Fecal samples from pigs in the early grower phase (day 80) were performed for microbial diversity, composition, and predicted functionality by using 16S rRNA sequencing. The results showed that no significant differences in microbial alpha diversity were observed between two RFI groups, whereas, some RFI-associated compositional differences were revealed. In particular, the microbiota of the LRFI group (more feed-efficient) had significantly higher levels of some members of Clostridiales and Bacteroidales (e.g., g_1_68 and g_norank_f_p_2534_18B5), which may promoted FE through protecting gut barrier function, compared with those of the HRFI pigs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis found that the LRFI pigs were likely have microbiota with higher levels of amino acid metabolism. Moreover, redundancy analysis (RDA) showed that litter size, parity, and date of birth had significant effects on the bacterial community structure. These results improved our knowledge of the porcine early-life fecal microbiota and its potential link underlying RFI, which would be useful for future development of microbial biomarkers for predicting and improving porcine FE as well as investigation of targets for dietary strategies.

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Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and Their Functional Annotations

Cited by 14 publications

References 81 publications

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Effect of host breeds on gut microbiome and serum metabolome in meat rabbits

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing

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