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A Bacterial Genome and Culture Collection of Gut Microbial In bioRxiv preprint doi: https://doi.org/10.1101/2021.08.18.456900; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A bacterial genome and culture collection of gut 2 microbial in weanling piglet 3 Bo Dong1,11, Xiaoqian Lin2,3,4,5,11, Xiaohuan Jing3,11, Tuanyuan Hu4,11, Jianwei 4 Zhou2,6, Jianwei Chen2,6,7, Liang Xiao2,4,7,8, Bo Wang3,9, Zhuang Chen1,10, Jing 5 Liu1,10, Yiyin Hu3, Guilin Liu6, Shanshan Liu2,6, Junnian Liu2,6, Wenkang Wei1,10*, 6 Yuanqiang Zou 2,4,7,8* 7 8 1 Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation 9 and Utilization, Agro-biological Gene Research Center, Guangdong Academy of 10 Agricultural Sciences, Guangzhou, 510640, China 11 2 Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 12 266555, China 13 3 China National Genebank, BGI-Shenzhen, Shenzhen 518120, China 14 4 BGI-Shenzhen, Shenzhen 518083, China 15 5 School of Bioscience and Biotechnology, South China University of Technology, 16 Guangzhou 510006, China 17 6 BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China 18 7 Laboratory of Genomics and Molecular Biomedicine, Department of Biology, 19 University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark 20 8 Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal 21 microbiome, BGI-Shenzhen, Shenzhen, China 22 9 Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, 23 Shenzhen, 518120, China 24 10 Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 25 510642, China bioRxiv preprint doi: https://doi.org/10.1101/2021.08.18.456900; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 26 11These authors contributed equally: Bo Dong, Xiaoqian Lin, Xiaohuan Jing, and 27 Tuanyuan Hu. 28 29 *Corresponding authors: 30 Wenkang Wei. 31 Address: Innovation Building, Agrogene-Centre, GDAAS, Guangzhou 510640, 32 China. 33 E-mail: [email protected] 34 Yuanqiang Zou. 35 Address: BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China. 36 E-mail: [email protected] 37 38 39 40 41 42 43 44 45 46 47 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.18.456900; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 48 49 ABSTRACT 50 The microbiota hosted in the pig gastrointestinal tract are important for 51 productivity of livestock. However, the individual species and functional 52 repertoires that make up the pig gut microbiome remain largely undefined. Here 53 we comprehensively investigated the genomes and functions of the piglet gut 54 microbiome using culture-based and metagenomics approaches. A collection 55 included 266 cultured genomes and 482 metagenome-assembled genomes 56 (MAGs) that were clustered to 428 species across 10 phyla was established. 57 Among these clustered species, 333 genomes represent potential new species. 58 Less matches between cultured genomes and MAGs revealed a substantial bias 59 for the acquisition of reference genomes by the two strategies. Glycoside 60 hydrolases was the dominant category of carbohydrate-active enzymes. 445 61 secondary metabolite biosynthetic genes were predicted from 292 genomes with 62 bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri 63 uncover the biosynthesis of reuterin was strain-specific and the production was 64 experimentally determined. These genomic resources will enable a 65 comprehensive characterization of the microbiome composition and function of 66 pig gut. 67 68 INTRODUCTION 69 Pigs are economically important livestock, widely used as monogastric animal 70 model for enteric microbiological studies, and serve as most consumed meat for 71 human worldwide1, 2. A large amount of microorganisms harbored in the gut of pig. 72 The research of gut microbiome of pig has increasingly advanced our understanding 73 of the role of the microbiota in feed conversion efficiency, pig health, and 74 production in recent years3, 4. bioRxiv preprint doi: https://doi.org/10.1101/2021.08.18.456900; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 75 Metagenomic studies have uncovered the genes, species, and functional diversity of 76 bacteria in mammalian intestines with the advantage in avoiding the time-consuming 77 of traditional culture-based approach and the inaccuracy of 16S rRNA sequences 78 analysis. A gene catalog consisting of 7.7 million non-redundant genes has been 79 constructed that draw a basic function map of the pig gut microbiota5. PIGC, the pig 80 integrated gene catalog, a recent expanded gene catalog comprised 17 million 81 complete genes that provide an expanded resource for pig gut microbiome research6. 82 Metagenomic binning is an essential tool for acquiring reference genomes readily, 83 particularly for uncultured microbiota, that has been widely used in study of human 84 gut microbiota, but rarely applied for pigs. However, misassembles and chimeric 85 contigs from MAGs result in substantial biases for the analysis of the gut 86 microbiome7, 8. These metagenomic studies have greatly increased our 87 understanding of pig gut microbiome6, 9. Nevertheless, the lack of bacterial isolates 88 and high-quality genomes limited our comprehensively understanding of the 89 structure and function of the gut microbiota of pig and the development of probiotics 90 for pig farming. 91 The culture-based approach has been well used for establishment of bacterial 92 collection for the human gut microbiota10. Over 1,500 species have been 93 successfully isolated from the human gut by using culturomics, introduced by Lagier 94 et al. and 247 new species have been unveiled11. Culture-based studies enable the 95 acquisition of both live bacteria and high-quality reference genomes and provide 96 experimental access for function exploration and intervention trials with probiotics. 97 PiBAC, a pig intestinal bacterial collection, was constructed by cultivation of 110 98 species and described 38 novel species from the gut of 19 pigs in Germany, United 99 States, and Canada12. This study highlighted the importance and necessity of 100 continuously isolating and characterizing microbial taxa from pig gut. 101 Here we performed a study of bacterial cultivation and genome sequencing along with 102 deep metagenome sequencing of 14 samples, including ileum and colon contents, and 103 feaces, from weanling piglets. A total of 266 isolated bacterial genomes and 482 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.18.456900; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 104 MAGs were obtained and investigated their functional repertoires. This study 105 provides a comprehensive view of the microbiome composition and the function 106 landscape of the gut of weanling piglets and a valuable bacterial resource for further 107 experimentations. 108 109 RESULTS 110 The metagenome sequencing described community composition of microbiota in 111 different gut regions of weanling piglets 112 A total of 42 samples, including 15 ileum contents, 18 colon contents and 9 faeces, 113 were collected from 42 weanling piglets from Guangdong Academy of Agricultural 114 Sciences. Every 3 samples from one line were combined into one sample which 115 ultimately resulted in 14 samples. To investigate the microbiota composition in each 116 sample, we first performed deep metagenomic sequencing for these samples and 117 generated 20 Gb of data for each sample on average. Notably, over 12% of reads 118 mapped to bacteria that could not be classified at the species level, which represent 119 novel species in the gut of weanling piglets (Supplementary Fig. 1). 99.8% of the 120 bacterial reads were assigned into 10 phyla. The phylum Firmicutes dominated the 121 gut microbiota in the ileum, colon, and faeces, accounting for 98.9%, 67%, and 76.8% 122 of the bacterial sequences, respectively (Figs. 1a, b). We also discovered 123 Lactobacillus were common present in 3 regions and accounted for the highest 124 proportion in samples from faeces and ileum and some samples from colon 125 (Supplementary Fig. 2a, b). The higher microbial diversity, including the Shannon 126 index, was observed in the colon as compared with the faeces and ileum (Fig. 1c), 127 consistent with previous studies13, 14. The principal coordinates analysis showed that 128 the microbiota composition of the faeces and colon were similar and were different 129 from that of the ileum (Fig. 1d). These results indicated the regional similarities and 130 differences in microbiota composition and the beneficial bacteria, like Lactobacillus 131 dominated the gut microbiota of weanling piglets, were valuable resource for the bioRxiv preprint doi: https://doi.org/10.1101/2021.08.18.456900; this version posted August 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 132 furtherly cultured-based study. 133 Bacteria culturing and genome sequencing of gut of weanling piglets 134 To advance our understanding of the diversity of gut microbiota and acquire bacterial 135 isolates from the weanling pig gut, we used a variety of culture methods, including 136 nutrient-rich medium (MPYG, with or without sheep blood), oligotrophic medium 137 (R2A), Columbia Agar, spore medium, etc. In total, 25 culture conditions were used 138 (Supplementary method). Most of the bacteria were cultured in sheep blood-MPYG, 139 MPYG, and sheep blood-spore medium.
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