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ORIGINAL RESEARCH

published: 23 December 2016
doi: 10.3389/fmicb.2016.02108

Evaluating the Contribution of Gut
Microbiota to the Variation of Porcine
Fatness with the Cecum and Fecal
Samples
Maozhang He, Shaoming Fang, Xiaochang Huang, Yuanzhang Zhao, Shanlin Ke,
Hui Yang, Zhuojun Li, Jun Gao, Congying Chen * and Lusheng Huang
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang,
China

Microbial community in gastrointestinal tract participates in the development of the
obesity as well as quite a few metabolic diseases in human. However, there are few
studies about the relationship between gut microbiota and porcine fatness. Here,
we used high-throughput sequencing to perform 16S rRNA gene analysis in 256
cecum luminal samples from Erhualian pigs and 244 stools from Bamaxiang pigs,
and adopted a two-part model statistical method to evaluate the association of gut
microbes with porcine fatness. As the results, we identified a total of 6 and 108
Edited by:
George Tsiamis, operational taxonomic units (OTUs), and 9 and 10 bacterial taxa which showed
University of Patras, Greece significant associations with fatness traits in the stool and cecum samples, respectively.
Reviewed by: Cross-validation analysis indicated that gut microbiome showed the largest effect on
Spyridon Ntougias,
Democritus University of Thrace, abdominal adipose by explaining 2.73% phenotypic variance of abdominal fat weight.
Greece Significantly more fatness-associated OTUs were identified in the cecum samples
Zakee L. Sabree,
than that in the stools, suggesting that cecum luminal samples were better used for
Ohio State University, USA
identification of fatness-associated microbes than stools. The fatness-associated OTUs
*Correspondence:
Congying Chen were mainly annotated to Lachnospiraceae, Ruminococcaceae, Prevotella, Treponema,
chcy75@hotmail.com and Bacteroides. These microbes have been reported to produce short-chain fatty acids
Specialty section:
by fermenting dietary indigested polysaccharide and pectin. The short-chain fatty acids
This article was submitted to can regulate host body energy homeostasis, protect host from inflammation and inhibit
Systems Microbiology, fat mass development. Our findings suggested that the gut microbiome may be an
a section of the journal
Frontiers in Microbiology important factor modulating fatness in pigs.
Received: 31 July 2016 Keywords: gut microbiome, fatness, swine, two-part model analysis, 16S rRNA gene
Accepted: 13 December 2016
Published: 23 December 2016
Citation: INTRODUCTION
He M, Fang S, Huang X, Zhao Y,
Ke S, Yang H, Li Z, Gao J, Chen C Obesity has been becoming one of the major health problems for humans, which is characterized by
and Huang L (2016) Evaluating
excessive fat accumulation, and imbalanced energy intake and expenditure, and accompanies with
the Contribution of Gut Microbiota
to the Variation of Porcine Fatness
low grade of systemic and chronic inflammation. It is associated with a wide range of pathological
with the Cecum and Fecal Samples. disturbances in metabolic organs and then predisposes toward type 2 diabetes mellitus (T2DM)
Front. Microbiol. 7:2108. (Hanning and Diaz-Sanchez, 2015) and cardiovascular disease (Kahn et al., 2006; Canfora et al.,
doi: 10.3389/fmicb.2016.02108 2015). Further, obesity is also related to certain types of cancer, osteoarthritis, and asthma. In pigs,

Frontiers in Microbiology | www.frontiersin.org 1 December 2016 | Volume 7 | Article 2108

. (2012) inferred that the gut microbiota might participate in the process of fat storage and should be correlated with the 16S rRNA Gene Sequencing and Quality porcine adiposity formation. Turnbaugh et al. In this Cecum 15 (18∗ ) 45 (73) 45 (99) 524 (2. Porcine Fatness-Associated Gut Microbiota fatness has been regarded as a typically complex and economic MATERIALS AND METHODS trait in pig production. et al. Both breeds show a higher unit (OTU) fatness than Western pig breeds (Ai et al. More and more studies in humans have libitum water.8% agarose gel by Guo et al. such as fermenting undigested energy and use of experimental animals established by the Ministry of substrates. The become a vigorous research area. 2006. such as genetics. In addition. Cani et al. The concentration and integrity of DNA were mice (Fei and Zhao... An endotoxin. Overall. The further studies showed fecal samples of the Bamaxiang population were harvested from that obesity is associated with the changes of two dominant the rectum before the pigs were transported to the slaughter phylum-level bacteria of Bacteroidetes and Firmicutes in the house. of bacterial diversity and the altered metabolic pathways were After transported to the laboratory.. The experimental pigs were slaughtered at 300 ± 3 days. 2009. 2002. dysbiosis of gut microbiota the melting temperature of 56◦ C with 30 cycles.. the samples were stored at demonstrated to associate obesity from a comparison study in −80◦ C freezer until used. and AbdomenFatWt) (Table 1) were separately measured by Backhed et al. Wall et al. electrophoresis. 2009).. All samples were collected in the 7-ml sterilized plastic gut (Mariat et al. we evaluated the association of the gut microbiome Feces 16 (17) 43 (55) 42 (57) 610 (1. Frontiers in Microbiology | www. The two pig populations were raised obesity. shoulder. Yang et al. Gut microbiota has demonstrated the the vernier caliper and electronic platform balance. and defined as ShoulderBF. 2005). The relationship between human obesity and gut microbiota composition has been established for Fecal and Cecum Luminal Sample several decades with the hallmark study by Backhed et al. The project was specially approved by participating in the metabolic processes. 2011). 2016). Malagelada. nutrition. and AverageBF) and fat mass (including LeafFatWt continuously interact with the host (Hooper et al.org 2 December 2016 | Volume 7 | Article 2108 . DNA was extracted from fecal and obese and lean twins (Turnbaugh et al. (2016) Control of Data identified tens of fatness-associated bacteria including Escherichia The V4 hypervariable region of 16S rRNA gene was selected and spp... All animals were healthy and did not receive shown that obesity is related to the gut microbiota (Ley any antibiotic treatment within 2 months before slaughter. luminal samples with QIAamp DNA Stool Mini Kit (Qiagen. stimulating the host immune system development. Wen et al. Dissection of the mechanism for Animals and Phenotype Measurement the fatness in pigs not only benefits the pig industry but A total of 244 Bamaxiang and 256 Erhualian pigs were also provides important information for understanding human used in this study. diverse. All animal great significance to animals by providing a large amount of works were conducted according to the guidelines for the care functions that host lacks. 2009. (2009). Fatness is affected by 14∼16% of crude protein.frontiersin. because pigs possess greater similarity with humans in the same farm house. 2013). ChestBF. Erhualian is another Chinese indigenous pig breed which is Sample Phylum Family Genus Operational taxonomic famous for its high prolificacy. 2006. But the mechanism remains controversial (Turnbaugh et al. preventing growth Animal Care and Use Committee (ACUC) in Jiangxi Agricultural of harmful and pathogenic bacteria and so on (Guarner and University. 8% of coarse fiber. which showed a higher relative abundance in high amplified by the fusion primers 515F [GTGCCAGCMGCCG fatness pigs. ∗ The numbers in brackets were the data before quality control. A reduction centrifuge tubes and dipped in liquid nitrogen immediately. Gerritsen et al. 2009. the The luminal contents of cecum were collected from the Erhualian role of the gut microbiota in the pathogenesis of obesity has population when pigs were killed in the slaughter house. (2004) which demonstrated that the gut microbiota as an Collection and DNA Extraction environmental factor modulates fat storage.038) study. and given an ad as gut microbiome.b).100 kJ of many factors. producing “obese microbe” was isolated from an obese human Germany) according to the manufacturer’s protocol (McOrist and was confirmed to cause the obesity in the germfree et al. chest and waist. and dynamic community of symbiotic microbes that WaistBF. (2008a. 2012). In pigs.. Munoz-Garach et al. and Luo et al. and lifestyle as well digestible energy and 0.85% of lysine.. and feces. 2013).660) with porcine fatness in both faces and cecum luminal samples.. The fatness traits including backfat thickness (measured at Mammalian gastrointestinal tract is resided by a complex.. All experimental pigs were fed in nutritional and metabolic physiology compared to other two times a day using the corn-soybean feed containing animal models (Swindle et al. 2002). accumulating evidences suggest that the CGGTAA] and 806R [GGACTACHVGGGTWTCTAAT] under endotoxin-induced inflammation. Since then. The DNA composition and Firmicutes/Bacteroidetes ratio are involved sequencing procedure was performed on the MiSeq platform in the development of obesity. Agriculture of China. 2007. the studies reported measured by the Nanodrop-1000 and the 0.He et al. 2008). It brings low feed conversion rate and unfavorable fat mass. 2003)... 3. TABLE 1 | Summary of gut microbial structure identified in the cecum and Bamaxiang is a Chinese indigenous mini pig breed.

and the quantitative model analyzed the effect of the the trait values corrected for sex and body weight and rm . The two-part model includes a binary model and a quantitative model. we performed this analysis at a series of different using an unweighted Z method. a total of n abundance of bacteria and the variables of environmental number of significantly associated OTUs was identified at a and host factors including pen. to obtain the clean sequence reads.11) was used to assemble the paired-end clean reads into weight. 000 ≤ 0. and sex certain P-value. 2010). SRR4431321. we repeated the cross- To further evaluate whether the effect came from the validation by 100 times and calculated the average value of presence/absence or the abundance of the gut microbiota or the explained variations. (CCA) using the R software with vegan package (Dixon.He et al.org 3 December 2016 | Volume 7 | Article 2108 . in less than 1% of the experimental pigs were removed from 2005). ACE. 2006).1. we split the data randomly into a 70% discovery set by Wilcoxon t-test. kinship. remained for the further association study between phenotypic value of fatness and relative abundance of gut microbiota in the two populations. Considering many microbes that may both.. SRR4454119. In brief. The possible correlations between the relative and a 30% validation set. In the discovery set. The formulas of the three models significant P levels ranging from 1. the risk of the gut microbiome on fatness traits (rm ) for each 2003). Data processing and quality control were processed k X √ by the standard protocols of bioinformatics analysis.1. We performed 1. batch. ensure the stability of the estimation. A total of 234 and 243 pigs which control the false discovery rate (FDR). Then. β1 and β2 are the estimated effects for the binary taxonomic unit (OTU) using the QIIME software (the toolbox and abundance effect. Binary Model : y = β1 b + e SRR4422947. we conducted a 100 times cross validation. USA) according to the manufacturer’s manuals.. The FDR control : FDR = N0 /N1 × 1. Those Z is the sum of these Zi divided by the square root of the OTUs which had relative abundance <0. FLASH Where y refers to the trait value (backfat thickness. Unweighted Z method : Z = zi / k ∼ N(0. N 1 is the number of the STATISTICAL ANALYSIS detected positive in the real analysis.5) reference association P-value. SRR4454082. Zi is the for Quantitative Insights Into Microbial Ecology). similarity) to perform the clustering (Edgar. 2015). and Shannon index were calculated by Mothur To test the phenotypic variation of porcine fatness explained software (Schloss et al.. k has a standard normal distribution (Whitlock.1% and were present number of tests.000 permutations.000× permutation tests to database (DeSantis et al. OTUs were matched to bacteria by using a quantitative analysis. Unique bacterial sequences for sex and body weight.0E – 05 to 0. 2011).1. SRR4431318. Explained by the Gut Microbiome Simpson. we rarefied the zi = ∅ −1 (Pi ) library size to 20. The comparison of α-diversity by gut microbiome.frontiersin. All were described as below: 16S rRNA gene sequencing data were submitted to the SRA database in NCBI with the accession numbers SRR4422912. 2009). The binary model accounted The phenotypic variance explained by the gut microbiome was for the effect of the presence/absence of the gut flora on porcine represented as the squared correlation coefficient (R2 ) between fatness.1 was set as had both phenotypes and 16S rRNA gene sequencing data were the significant threshold.2. which uses Z-transform test converting the one tailed P-values. According to the report by Fu et al. 1). To abundance of the microbes on porcine fatness. Frontiers in Microbiology | www. Microbial Diversity Analysis Estimating the Phenotypic Variance The α-diversity indexes of chao1. further analysis.000 clean reads depth. And then. fatness. Pi was UCLUST (an algorithm to cluster sequence reads based on from each of k independent tests into standard normal deviates. animal in the validation set was calculated using an additive model: Two-Part Model for Association Analysis n To identify the gut microbes which were associated with porcine rm = X (β1 + bj + β2j qj ). low-quality. SRR4422951. observed species. indexes between Bamaxiang and Erhualian pigs was performed Thus. leaf fat (v. and barcode sequences. and e represents the residuals. and abdominal fat weight) per individual after adjusting tags (Magoc and Salzberg.1. The FDR ≤ 0. q is a quantitative with 97% sequence similarity were clustered as operational feature. The minimum of the P-values from the binary analysis. (2015). and Quantitative Model : y = β2 q + e SRR4431322. and the effect sizes of binary and quantitative were examined by canonical correspondence analysis features of each OTU (β1 and β2 ) were estimated before. b is a binary feature. and meta-analysis was set as the final primer-specific version of the GreenGenes (v13. Where N 0 is the average number of the detected significance at a certain P cutoff in 1. Porcine Fatness-Associated Gut Microbiota (Illumina. we performed the association studies with two-part j=1 model (Fu et al. a combination of the binary and quantitative analysis was contribute a small effect but may not be confidently detected at characterized by a meta-analysis in which the P-value was derived FDR ≤ 0. we used custom scripts j=1 to remove the primer. SRR4431319. SRR4422914.

The phenotypic values were Frontiers in Microbiology | www. Porcine Fatness-Associated Gut Microbiota FIGURE 1 | Comparison of the α-diversity of gut microbiome between cecum and fecal samples.05). 2. ∗∗ P < 0. respectively (Table 1). the numbers of microbial phylum and genus were 18 Associated with Porcine Fatness in the and 99.005.000 abundances of the phyla Firmicutes and Spirochaetes.He et al. Escherichia.888 (an average of 28. leaf fat weight and abdominal that all five indexes showed significant difference (P = 6. The microbial richness and diversity were showed significant difference between cecum and feces (∗ P < 0.00001. The tags were annotated to microbial taxa. The fecal samples had a significantly higher Microbial Diversity in Porcine Cecum α-diversity (Figure 1).frontiersin.90E − 03. CF231. Wilcoxon t-test). luminal samples were 8. We compared the α-diversity of Cecum and Fecal Samples microbiota between cecum and feces samples using the chao1. Streptococcus.038 OTUs. per sample) and 7. observed species. We further compared the phylogenetic composition of the microbial community at the phylum and and Feces genus level. In the Erhualian Identification of Gut Microbes population. 99% of the total clean reads in each sample.597 reads per and Prevotella.96E − 50. In the Bamaxiang population. The summary description of phenotypic values of backfat ACE. a total of 17 phyla and 57 genera were identified. The genera Lactobacillus. These OTUs occupied microbial composition of both cecum and feces (P < 0. fat weight is shown in Table 2. RESULTS 1.05). The cecum luminal samples had significantly The total numbers of sequence reads for fecal and cecum higher abundances of the phyla Bacteroidetes and Proteobacteria. and 3.976 (an average of 30.org 4 December 2016 | Volume 7 | Article 2108 . we focused on the 610 and 524 OTUs in the Bamaxiang identified the significant effects of host gender and batch on the and Erhualian population. and found thickness (subcutaneous fat). However. After quality (Figure 2). Canonical correspondence analysis (CCA) showed that host gender and batch had significant effects on microbial composition (P < 0.660 and 2.05) two pig cohorts obtained 1. We performed CCA analysis in the tested samples and control. the fecal samples showed the higher sample). and Treponema (P < 0.766 reads and the genera Akkermansia. Shannon and Simpson index.320. respectively).76E − 05. We rarefied the library size to 20.64E − 52. the diversity was evaluated by Shannon and Simpson index. and the reads per sample to reduce the effect of sequencing depth.029.0001. ∗∗∗ P < 0. respectively.20E − 55. chao and ace index. The gut microbial richness was estimated by observed species. 5. Bacteroides. respectively.

He et al. (B) At genus level. (A) At phylum level.org 5 December 2016 | Volume 7 | Article 2108 . Porcine Fatness-Associated Gut Microbiota FIGURE 2 | Comparison of the relative abundance of gut microbiota between cecum and fecal samples.frontiersin. Frontiers in Microbiology | www.

These six OTUs samples (P = 1.72 1.1. we identified six OTUs (Otu363. more and more researches have concentrated FDR ≤ 0.37 ± 0. The species Mucispirillum increased to P = 0. The other six associations level.89) and abdominal fat weight in the cecum luminal associated with leaf fat weight at FDR ≤ 0. ShoulderBF.61% in identified in this study.1. While nine by WaistBF and AverageBF.org 6 December 2016 | Volume 7 | Article 2108 .59E−04 and 7.31 ± 0. 1.09% phenotypic variation of LeafFatWt in the validation set.2–1. the OTUs annotated to the Ruminococcaceae were showed positive associations with fatness traits.55% in AverageBF. The strongly negative associations with LeafFatWt for Bamaxiang pigs. Of the 10 fatness- associated taxa.78 2.6 0.3 to the Lachnospiraceae. leaf fat weight. Otu1330. and 2. we did not detect any OTUs significantly associated and metabolic dysfunctional diseases in both humans and mice. since gut microbiome has been reported to associate obesity However.61 1. both types of samples.3 annotated to the Prevotella. Lachnospiraceae. Of the 11 associations. 1. We observed that Bamaxiang (n = 234) Erhualian (n = 243) these OTUs were mainly annotated to the YS2 (Cyanobacteria). ChestBF. five were detected by the binary analysis.69 0.96 ± 0. waist backfat thickness.0E − 05 level.7 3.58 2. abdominal fat weight.4–5. and 2. ShoulderBF. one by firstly adjusted for the effects of sex and body weight. Lachnospiraceae. for and WaistBF. Further.1 4. WaistBF.87 1.9–7. WaistBF and AverageBF.02 ± 0. especially with the samples from cecum. We did not detect any were annotated to unclassified Ruminococcaceae. and the quantitative analysis and four by the meta-analysis. and three by AbdomentFat no such studies have been reported in pigs. While only one significant association cross-validation analysis by splitting the data set randomly into was found for each of LeafFatWt. we evaluated the association of the gut microbiome specifically associated with only one phenotype. ShoulderBF. We did not identify any significant associations at OTU level for other fatness traits (Supplementary Table 1).68E − 04.2–5. We did not identify any significant associations with ShoulderBF and AverageBF. And both positive and WaistBF (cm) 2. 19 with the AverageBF and 55 with AbdomenFatWt. we identified LeafFatWt (kg) 2.1 negatively associated with fatness traits. and Fatness traits Mean ± SD Range Mean ± SD Range Bacteroides.72 ± 0. and WaistBF an 70% discovery set and a 30% validation set at the OTU (Figure 3A. average backfat thickness. and AverageBF). To our knowledge. Of the 80 fatness-associated Exploring the effect of the gut microbiome on obesity and insulin OTUs.07 ± 0. Otu393. significant associations. Prevotella. Fatness is an importantly economic trait in pig production. 30 with upon the microbiota inhabiting the host gastrointestinal tract WaistBF.1 and the risk model included more (but less schaedleri was the only member of the phylum Deferribacteres significant) OTUs. two (Otu148 and Otu162) were shared by four traits resistance has gained insight into the role of the microbiota in (AbdomentFat. with ChestBF and LeafFatWt. six for AbdomenFatWt.23 0.1.29% of respectively).32 0.72 0. we found that the OTUs identified were detected for abdomimal fat weight (AbdomenFatWt).73E − 04. respectively. In the Bamaxiang pigs.82 1. Prevotella.76 ± 0. then the residuals were used for association analyses. two were identified by the quantitative analysis (the abundance of bacteria) and one by meta-analysis.2–1.75% AbdomenFatWt were identified on this microbe from phylum in WaistBF. and Bacteroides were ChestBF (cm) 4. the explained variance increased to 1. AbdomenFatWt.58 0.96 ± 0.73% phenotypic variation of ChestBF and AverageBF (P = 1.10E − 04). including one for WaistBF. and Otu500) that were significantly Z_score = 3.00E − 04). Treponema.73). ChestBF. OTUs were shared by AbdomentFat.80 ± 0. In the Erhualian cohort. Otu95. and two for LeafFatWt (Figure 3B.6 negative associations were observed for the OTUs annotated AverageBF (cm) 3. and species R. chest backfat thickness.5 2.8–6. WaistBF.96 ± 0.3–5. Otu206. Ruminococcaceae.8–3. and 1. three the development of diabetes mellitus and cardiovascular disease.8 at FDR ≤ 0. gnavus was positively associated AbdomenFatWt.4–5. DISCUSSION With respect to the cecum luminal samples. a total of 108 significant associations for 80 unique OTUs were found at For recent years. the fatness- respectively). Supplementary Table 2). of these 11 for Erhualian pigs (Figure 5).79 ± 0. Those ShoulderBF (cm) 4. AverageBF. At the Phenotypic Variance of Porcine Fatness taxonomic level. Frontiers in Microbiology | www. LeafFatWt. both WaistBF and AverageBF (P = 6. 1. we identified 11 significant associations related Explained by Gut Microbiome to nine unique taxonomies for fatness traits at the significant To investigate how much degree of phenotypic variance of fatness threshold of FDR ≤ 0. at P = 1. Z_score = 3. Treponema.6–5. In Ruminococcus gnavus showed a positive association with the fecal samples. Firmicutes. Actinobacteria showed a negative association with 1.11% of AverageBF. including four associations with ShoulderBF.9 2. one for ChestBF. At the taxonomic level.7–4. and Clostridiales.He et al.41% in AbdomenFatWt to species level (P = 1. When the significance threshold of association with LeafFatWt (P = 1.00E − 04. both leaf fat weight in the fecal samples (P = 1.7 10 taxa that were significantly associated with fatness traits AbdomenFatWt (kg) 0. Coprobacillus was positively associated with both associated OTUs can explain 0.88E − 04. The detailed with fatness in swine.07% in ShoulderBF.1.frontiersin. Porcine Fatness-Associated Gut Microbiota TABLE 2 | Summary description of phenotypic values of porcine fatness annotation results for the fatness-associated OTUs are shown traits in the Bamaxiang and Erhualian population. 1.0E − 05 level in the discovery set could explain more details.7 3. For at P = 1.47 ± 0. In addition. Ruminococcus other taxa that showed the significant association with fatness in gnavus. shoulder backfat thickness.5–6. Each of the other fatness-associated OTUs was the first time.89 0. we conducted a 100 times identified for AverageBF.91E − 04 and 2.53% of WaistBF. in Supplementary Table 3 and Figure 4. eight were detected by the binary analysis (presence/absence). two were was explained by the gut microbiome. Supplementary Table 2).

Compare with the fecal samples. microbes (Eckburg et al. This should be explained by (1) different identified for each fatness trait (Qiao et al. (2) different genetic background significantly higher number of the fatness-associated OTUs was between two pig cohorts.He et al. Microbiota in stool are a mix our knowledge.. association analysis to interpret effects of both presence/absence This heterogeneity may be caused by distinct mechanism of and relative abundance of gut microbiota on porcine fatness. Porcine Fatness-Associated Gut Microbiota FIGURE 3 | The effect of bacterial taxonomies on abdominal fat weight. Dashed circles indicate the scale of Z or T-values from 1 to 5. Moreover. To the best of sampling sites (cecum vs. As we have well known. and average backfat thickness. fat deposition for different types of adipose involving different As we expected. and average backfat thickness are shown as Z or T scores in the feces (A) and cecum (B). although all experimental pigs were raised microbes among abdominal adipose. leaf fat weight. we adopted a novel and powerful two-part model We noticed that most of the associations were trait-specific. this study first evaluated the fatness-associated mucosally associated microbes. 2005). in which different genomic loci were among samples. The different color sectors indicate positive or negative associations and their significance level.frontiersin. most from the colon and lumenal microbes in the cecum samples. respectively. leaf fat and subcutaneous in the same farm house and fed the similar formula diet. Frontiers in Microbiology | www. 2015). feces). leaf fat weight. This condition was similar to that in genetic dissection observed distinct phylogenetic composition of gut microbiome of porcine fatness traits. we adipose.org 7 December 2016 | Volume 7 | Article 2108 .. The effects of bacterial taxonomies on abdominal fat weight. identified in the cecum samples.

tract. 2013). Frontiers in Microbiology | www. A recent study found that the α-galactosidase M. the abundance of Mucispirillum was decreased (Clarke played an indispensable role in the degradation of dietary et al. The et al.org 8 December 2016 | Volume 7 | Article 2108 . as a kind of probiotics. 2014). A previous study indicated that the taxa have been reported to participate in the process of the Anaerovibrio lipolytica from Anaerovibrio can produce lipase in utilization of undigested carbohydrates from the diets or the hydrolysis of triglyceride (Henderson.. butyricum associated with fatness traits in both fecal and cecum samples. and then the SCFAs were absorbed by the host and could Interestingly.. in this study have potential functions related to metabolisms. Both Anaerovibrio and Clostridium butyricum were negatively At the taxonomic level. both R.. 2013). R. some of the fatness-associated bacterial associated with LeafFatWt. Andoh et al. 2014. Previous studies host polysaccharide. gnavus and and polysaccharides occurs at the cecum. many fatness-associated microbiota identified regulate host body energy homeostasis (Layden et al. The studies in human and rat found that and antivirals for humans (Mahajan and Balachandran. producer of many bioactive metabolites including antibacterials Tison et al. can produce butyrate that provides the majority energy to R. 2016).frontiersin. gnavus was positively have summarized that. Zhang et al. The percentages were calculated with (the number of the fatness-associated OTUs annotated to a given bacterial taxonomy/80 × 100%). 2013).. which regarded as a supplement of the bile acid (Lee by virus (Araki et al. gnavus mice. Interestingly. 2002.. Actinobacteria which was negatively associated with oligosaccharides and exerted a tremendous fascination on both average and waist backfat. 2011). And fermentation of dietary indigestible fiber et al. For examples. has been recognized as the designing of galacto-oligosaccharide (GOS) prebiotics (Cervera. Furthermore. Porcine Fatness-Associated Gut Microbiota FIGURE 4 | The bacterial annotation of the 80 fatness-associated operational taxonomic units (OTUs) in the Erhualian population based on the Greengenes database. 2004. in the diet induced obesity (DIO) of the glycoside hydrolase (GH) family from R. gnavus was enriched in the obese rats and humans (Petriz et al.. 2011).He et al. 2012). We suggested that Coprobacillus identified in this study could ferment the indigested the samples from the cecum would be better for studying the polysaccharide into the SCFAs from the food in gastrointestinal association between microbiota and fatness than stool samples. gnavus plays a pivotal role in UDCA formation in the the gut epithelial and repairs the intestinal mucosa damaged colon. C.... cecum has the great diversity and complex of microbiota (Looft R. schaedleri was negatively associated with AbdomenFatWt in 1 (Aga1) and α-galactosidase 2 (Aga2) which are two kinds fecal samples. 1971).

He et al. The figures show the variation of fatness trait values explained by gut microbes at different significance levels in the Bamaxiang (A) and Erhualian (B) pig population. Porcine Fatness-Associated Gut Microbiota FIGURE 5 | The contribution of gut microbiome to pig fatness traits based on the associated OTUs. Frontiers in Microbiology | www.frontiersin.org 9 December 2016 | Volume 7 | Article 2108 .

(2013) described et al. (2012) observed that Ruminococcaceae an efficient methodology for predicting complex traits from was enriched in mice fed high fat diet.org 10 December 2016 | Volume 7 | Article 2108 . Although the effect size of gut microbiome on fatness role of biohydrogenation. 2015). and Bacteroidales However. Perry et al. which may exert potential factor for porcine fatness. Kovatcheva-Datchary et al.. 2014). 2013. which contain a set of in cattle with high accuracy. Members 2015).. Treponema. et al. such as diets within the group with the production of butyric acid (Duncan displayed less effects on gut microbiome and the subsequent fat et al.. These porcine fatness that would provide basic information for microbes ferment polysaccharides to short-chain fatty acids. and demonstrated that also observed a higher abundance of Ruminococcaceae in the microbiome profiles can be used to predict human inflammatory db/db mice compared to lean mice. and provide a new insight fermenting glucose and indigestible diet fiber (Miller and Wolin.. Significantly higher number of fatness-associated associated with fatness traits. Ruminococcus. 2002.73% and Ahmad. 2000. In the futural study. 2007. 2010. These bacteria were identified effect size of gut microbiome on porcine fatness is not very in a phylo-functional core of gut microbiota in healthy young large in this study. Ruminococcaceae has been reported to play the deposition. Geurts et al. (2011) quantitative microbiome profiles. Crost et al. Barcenilla et al. traits. Bacteroides. Lachnospiraceae. OTUs were identified in the cecum suggesting that cecum In addition. pig production by reducing fat mass and improving the feed but also protect them from inflammation and noninfectious efficiency. Delzenne and Cani. Maslowski et al.. ingestion ETHICS STATEMENT of high fat diet was associated with the higher abundance of Clostridiales compared to the low fat diet regardless of propensity All samples were collected according to the guidelines for the care for obesity (de La Serre et al. The fatness-associated microbiota Bacteroides-prevotella also showed a negative correction with were mainly involved in fermenting dietary indigestible fiber fat mass development and inflammation (Neyrinck et al. This effect At the OTU level. This different contribution size should be due to the reason of this family have been linked to obesity in humans (Cho that all experimental pigs were raised in the same farm house and et al. the SCFAs can influence host homeostasis.. and luminal samples would be better used for investigation of Clostridiales were also annotated to the fatness-associated fatness-associated microbes than stool samples. from succinate pathway pigs. We identified a number of taxa and OTUs that showed inhibit the accumulation of fat mass development in adipose significant associations with porcine fatness traits in the cecum tissue and promote leptin level. Ivarsson et al. (2010) used partial least square a host mutualistic component to help to degradate dietary discriminate analysis (PLS-DA) to predict host genotypes. the results from this study gave colonic diseases. the construction (Warnecke et al. (2016) reported that the increased acetate could promote hyperphagia and increase energy storage as fat. the fatness-associated OTUs were size was similar to that of most quantitative trait loci (QTL) mainly annotated to YS2 (Cyanobacteria). 2015). (2010) of prediction methodology based on the gut microbiome proposed that the degrading polysaccharide-rich diet allowed profiles for porcine fatness traits would greatly promote the gut microbiota to maximize energy intake from fibers diets. In mice. Besides Prevotella and Treponema. Lachnospiraceae is abundant in the digestive tract pivotal contributing factor in diet-related obesity (Zhang C. In the cecum acids have been reported to inhibit fat mass development and samples.. Coprococcus. we have established that gut microbiome should be a risk via fermenting various substrates. 2009. The environmental factors. regulating the gut microbiome to reduce fat deposition in such as propionate by Bacteroides spp. 2012). 2002).frontiersin. and use of experimental animals established by the Ministry of Frontiers in Microbiology | www. diets fiber which could produce significantly more short-fatty acids or obesity phenotypes..55–2. of the variation in the six fatness-associated traits. Onrust A recent study reported by Ross et al. Kim et al. mainly due to the association of many species provided the same diet. et al. and act as gut microbiota. In addition. Ruminococcaceae... and acetate by Prevotella spp. The short-fatty Ridaura et al. Prevotella. and polysaccharides to produce short-fatty acids. of many mammals and relatively rare elsewhere. 2011. into the role of gut microbes in affecting the porcine fatness 1996. Furthermore. luminal samples and feces. These results help us and Ruminococcus have been reported to produce acetate via to better understand the structure and functional potential of acetyl-CoA from pyruvate and Wood–Ljungdahl pathway by swine gastrointestinal microbiota. from pyruvate via acetyl-CoA. and Treponema were negatively inflammation.. And based on the phylotypes of bacterial genes for cellulose and xylan hydrolysis. Blautia. we established that gut microbiome should Chinese cohorts (Zhang J. In diet-induced obese mice. 2009).. The members of Blautia be a risk factor for porcine fatness. 2008). Although the OTUs in the cecum samples. Zhang et al. gut microbiota has been implicated as a (Figure 3).. (2013) showed that the interactions of acetate and propionate with GPR43 have an CONCLUSION important role in anti-inflammatory effects via the modulation of cTReg cell. Bacteroides important cues for isolation of the causative microbes for was also annotated to the fatness-associated OTUs. and is capable of producing butyrate is small. Pryde et al. 2008.He et al.. 2011).. (2009) and Smith et al. Liu et al.. 2012). physiological functions in host health (Huws et al. Porcine Fatness-Associated Gut Microbiota and growth promoting substances for plants and animals (Atta We estimated that gut microbiome could explain 1. Prevotella and Treponema bowel disease (IBD) status and BMI. Prevotella. in humans. and methane production belong to xylan-degrading bacteria. De Filippo et al.. Flint et al. previously reported for porcine fatness traits (Ai et al.. 2013). 2011.

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