microorganisms Article Comparison of Productivity and Fecal Microbiotas of Sows in Commercial Farms Haruka Uryu 1,2, Takamitsu Tsukahara 3 , Hiromichi Ishikawa 4, Munetaka Oi 4, Satoshi Otake 4, Itsuro Yamane 5 and Ryo Inoue 1,2,* 1 Laboratory of Animal Science, Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan; [email protected] 2 Laboratory of Animal Science, Department of Applied Biological Sciences, Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan 3 Kyoto Institute of Nutrition & Pathology, Kyoto 610-0231, Japan; [email protected] 4 The Japanese Association of Swine Veterinarians (JASV), Ibaraki 300-1260, Japan; [email protected] (H.I.); [email protected] (M.O.); [email protected] (S.O.) 5 National Agriculture and Food Research Organization (NARO) (National Institute of Animal Health), Ibaraki 305-0856, Japan; iyamane@affrc.go.jp * Correspondence: [email protected]; Tel.: +81-(0)-728965469 Received: 31 August 2020; Accepted: 23 September 2020; Published: 24 September 2020 Abstract: Sow productivity, that is, the number of weaned piglets per sow per year, depends on their health status. The gut microbiota is considered a crucial factor in the health of pigs and may affect sow productivity. In the present study, we aimed to investigate the relationship between productivity and the fecal microbiotas of sows in different farms. Feces of sows were collected from 18 farms (10 samples/farm). A total of 90 fecal samples of high-reproductive performance farms were labeled as group H, and 90 fecal samples from low-reproductive performance farms were labeled as group L. Fecal microbiotas were analyzed by 16S rRNA metagenomics, and the organic acids and putrefactive metabolites of the microbiotas were measured. β-diversity was significantly different between groups H and L (p < 0.01), and the relative abundances of 43 bacterial genera, including short-chain fatty acid-producing and fiber-degrading bacteria such as Ruminococcus, Fibrobacter and Butyricicoccus, significantly differed between groups (p < 0.05). In addition, the concentrations of acetate, propionate and n-butyrate were significantly higher in group H than in group L (p < 0.05). In conclusion, sow productivity in farms was likely associated with the compositions of the fecal microbiotas. Keywords: sow productivity; fecal microbiota; gut microbiota; short-chain fatty acid; fiber degrading; farm 1. Introduction The number of piglets produced per sow in a year depends on the sow’s reproductive performance [1]. In addition, the number of weaned piglets per sow in a year, a major productivity parameter, is defined by several factors such as the number of piglets born alive, the number of surviving piglets during suckling, as well as the days of recurrence to estrus and the pregnancy rate of the sow [1]. Therefore, “the number of weaned pigs/sow/year” is also considered a major parameter to evaluate farm productivity [2]. During lactation, the loss of body condition in sows induces a delay in the recurrence to estrus, and subsequent decreases in the pregnancy rate and the litter size [3]. Moreover, increases in stress in prepartum sows cause lower maternal endogenous hormone levels and negatively affect the farrowing performance, mostly due to prolonged birth intervals [4]. Therefore, the health conditions of sows directly affect their reproductive performance. The gut microbiotas are the bacterial populations that reside in the intestinal tract of the host. The number of bacteria in the gut microbiotas of mammals is estimated to be approximately 1014 [5,6], Microorganisms 2020, 8, 1469; doi:10.3390/microorganisms8101469 www.mdpi.com/journal/microorganisms Microorganisms 2020, 8, 1469 2 of 12 which maintain a relatively stable crosstalk with their complex ecosystem. The gut microbiota exerts certain beneficial effects on the host. For example, bacteria in the gut microbiota produce beneficial metabolites such as short-chain fatty acids (SCFAs) that control the proliferation and differentiation of epithelial cells, develop and maintain the homoeostasis of the immune system, and protect the host from pathogens [7,8]. Nonetheless, given the opportunity, some bacteria in the microbiota and their metabolites can adversely affect the host [9–11]. In other words, the bacteria in the gut microbiota can be both beneficial and harmful to the host. The gut microbiota of the pig can also be regarded as a crucial factor in the pig’s health, as it affects the function of the intestinal barrier, the development of the immune system, and the efficiency by which feed is used [12]. Previous work has shown that growing pigs with high-feed efficiency exhibit specific bacterial compositions of their gut microbiotas [13–15]. This evidence seems to suggest that the gut microbiotas in growing pigs are associated with their growth performance by promoting healthy intestinal environments. In addition, previous studies showed that status of the gut microbiotas of sows is associated with their reproductive performance [16,17]. However, those studies were carried out in one single farm, focusing solely on finding differences in the productive performance of individual pigs, not between pig farms. In general, pigs in commercial farms are not managed individually, but per pen, house or farm [18]. Farmers and veterinarians only act and respond when an adverse event in a given pig unit occurs to prevent pathogen infections or changes in the feeding strategy, water quality and stress care [19]. Therefore, we theorized that the indigenous gut microbiotas of sows within a farm would be similar, and hence, more closely associated with sow productivity within the respective farm than with individual pigs. In the present study, we aimed to investigate the relationship between sow productivity and the fecal microbiota of pigs in different farms. We also investigated the relation between sow productivity and the metabolites in the gut microbiota such as SCFAs, phenol, indole, skatole and para-cresol, because we also theorized that these metabolites may affect the health of sows. To the best of our knowledge, this is the first work to study the relationship between the fecal microbiotas of sows and sow productivity at a farm level. For practical purposes, in the present study, the number of pigs produced per sow/year, that is, the breeding ability of sows, was defined as “sow productivity”. 2. Materials and Methods 2.1. Animals and Sampling Pigs from 18 commercial swine farms were used in the present study. These farms were included in the database survey of PigINFO 2017. PigINFO is a benchmarking system operated by the Japanese Association of Swine Veterinarians (JASV) and the Agri-Food Business Innovation Center of National Agriculture and Food Research Organization [20]. In 2017, 162 farms were included in the database. Of all farms, 18 farms were selected, as per breeding lines (L W or W L) and × × reproductive performance (the mean number of piglets weaned per sow/year). Nine farms were from the top tier (top 25% of farms) and 9 from the lowest tier (bottom 25%) of the reproductive performance range. We obtained the consent and fecal samples of 10 sows/farm from the owners of the 18 farms. All experimental procedures were followed in accordance with the guidelines issued by the Ministry of Education, Culture, Sports, Science and Technology-Japan and Science Council of Japan. The experiments were exempted from ethic evaluations because all animals used were commercially raised and reared in a conventional swine farms under the supervision of the local veterinary and the samples were collected on site. Fecal samples were collected fresh from 10 healthy multiparous sows (2nd–5th parity) with fresh feces and used as the fecal samples. Feces during or immediately after defecation was collected by a sterilized fecal collection tube (80.623; SARSTEDT, Tokyo, Japan). When feces fell down onto the ground, the portion that did not touch the ground was carefully chosen and collected. The fecal samples were stored at 80 C until further use. Ninety fecal − ◦ Microorganisms 2020, 8, 1469 3 of 12 samples from the high-reproductive performing farms were labeled as the high-performance group (group H), and the remaining 90 fecal samples were labeled as the low-performance group (group L). The seven reproductive performances parameters used in the present study are shown in Table1. Table 1. Parameters of reproductive performance in high- and low-reproductive performance groups. Parameters of Reproductive Group H (n = 9) Group L (n = 9) Welch’s t-Test p Values Performance Number of piglets weaned/sow/year 27.69 0.33 19.33 0.62 5.3 10 8 ± ± × − Farrowing rate 0.89 0.01 0.80 0.02 2.7 10 3 ± ± × − Farrowing/sow/year 2.41 0.02 2.21 0.02 4.3 10 6 ± ± × − Number of piglets born/litter 14.68 0.43 11.48 0.30 2.4 10 5 ± ± × − Number of piglets born alive/litter 13.27 0.33 10.24 0.32 6.9 10 6 ± ± × − Number of stillbirths/litters 1.42 0.14 1.23 0.17 0.42 ± ± Pre-weaning mortality 0.13 0.02 0.15 0.02 0.53 ± ± Farrowing rate: Farrowing of inseminated sows. Parameters with significant differences between groups H and L are shown in bold (p < 0.05). Mean SE is shown. ± 2.2. Analysis of the Fecal Microbiota by 16S rRNA Metagenomics Extraction of bacterial DNA from fecal samples, library preparation and deep sequencing by MiSeq (Illumina, Tokyo, Japan) were carried out exactly as described by Inoue et al. [21]. The obtained sequence data were analyzed as per the protocol reported by Inoue et al. [21]. 2.3. Measurement of the Concentrations of Organic Acids in Fecal Samples The number of samples with measurable organic acid concentrations were 87 in group H and 88 in group L, because the volumes of three samples in group H and two in group L did not suffice for measurement.