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Amino acid utilization allows intestinal dominance of Lactobacillus amylovorus

The ISME Journal (2022)Cite this article

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Abstract

The mammalian intestine harbors heterogeneous distribution of microbes among which specific taxa (e.g. Lactobacillus) dominate across mammals. Deterministic factors such as nutrient availability and utilization may affect microbial distributions. Due to physiological complexity, mechanisms linking nutrient utilization and the dominance of key taxa remain unclear. Lactobacillus amylovorus is a predominant species in the small intestine of pigs. Employing a pig model, we found that the small intestine was dominated by Lactobacillus and particularly L. amylovorus, and enriched with peptide-bound amino acids (PBAAs), all of which were further boosted after a peptide-rich diet. To investigate the bacterial growth dominance mechanism, a representative strain L. amylovorus S1 was isolated from the small intestine and anaerobically cultured in media with free amino acids or peptides as sole nitrogen sources. L. amylovorus S1 grew preferentially with peptide-rich rather than amino acid-rich substrates, as reflected by enhanced growth and PBAA utilization, and peptide transporter upregulations. Utilization of free amino acids (e.g. methionine, valine, lysine) and expressions of transporters and metabolic enzymes were enhanced simultaneously in peptide-rich substrate. Additionally, lactate was elevated in peptide-rich substrates while acetate in amino acid-rich substrates, indicating distinct metabolic patterns depending on substrate forms. These results suggest that an increased capability of utilizing PBAAs contributes to the dominance of L. amylovorus, indicating amino acid utilization as a deterministic factor affecting intestinal microbial distribution. These findings may provide new insights into the microbe-gut nutrition interplay and guidelines for dietary manipulations toward gut health especially small intestine health.

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Fig. 1: Structure and composition of gut microbiota in pigs fed with intact casein or hydrolyzed casein.
Fig. 2: Measurement of bacterial quantities and peptide-bound amino acids.
Fig. 3: Identification and genomic sequencing of L. amylovorus S1 from the small intestine of pigs.
Fig. 4: Growth traits and utilization of peptide-bound amino acids by L. amylovorus S1 in amino acid-rich or peptide-rich substrates in vitro.
Fig. 5: The utilization, transport and metabolism of free AAs by L. amylovorus S1 in vitro.
Fig. 6: Distinct metabolic patterns in amino acid-rich or peptide-rich substrates during in vitro cultivation.
Fig. 7: Summary of the amino acid utilization in L. amylovorus.

Data availability

The 16S rRNA gene sequence of L. amylovorus S1 has been submitted to NCBI under the accession number MT525371. The high-throughput sequencing data are available under PRJNA796201 within NCBI Sequence Read Archive. The complete sequence of L. amylovorus S1 is available at GenBank under the accession number: CP090603 (chromosome), CP090604 (plasmid 1) and CP090605 (plasmid 2).

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Acknowledgements

This work was supported by National Natural Science Foundation of China (32030104, 31902166).

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Author notes

  1. These authors contributed equally: Yujia Jing, Chunlong Mu.

Authors and Affiliations

  1. Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China

    Yujia Jing, Chunlong Mu, Huisong Wang, Junhua Shen, Erwin G. Zoetendal & Weiyun Zhu

  2. National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China

    Yujia Jing, Chunlong Mu, Huisong Wang, Junhua Shen, Erwin G. Zoetendal & Weiyun Zhu

  3. Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands

    Erwin G. Zoetendal

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Contributions

WZ conceived, designed, supervised the study and proposed the manuscript strategy. YJ conducted the experimental work and performed statistical tests with guidance from CM and EGZ. CM wrote the manuscript draft with revisions and edits by YJ, EGZ and WZ. WZ and CM finalized the manuscript. HW and JS conducted the animal study. All the authors have read and approved the final manuscript for publication.

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Correspondence to Weiyun Zhu.

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Jing, Y., Mu, C., Wang, H. et al. Amino acid utilization allows intestinal dominance of Lactobacillus amylovorus. ISME J (2022). https://doi.org/10.1038/s41396-022-01287-8

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