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Microbial Ecology

Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves

Yuanting Zhu, Jinxin Liu, Julian M. Lopez, David A. Mills
Shuang-Jiang Liu, Editor
Yuanting Zhu
aDepartment of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, California, USA
bFoods for Health Institute, University of California, Davis, Davis, California, USA
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Jinxin Liu
aDepartment of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, California, USA
bFoods for Health Institute, University of California, Davis, Davis, California, USA
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Julian M. Lopez
aDepartment of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, California, USA
bFoods for Health Institute, University of California, Davis, Davis, California, USA
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David A. Mills
aDepartment of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, California, USA
bFoods for Health Institute, University of California, Davis, Davis, California, USA
cDepartment of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, California, USA
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Shuang-Jiang Liu
Chinese Academy of Sciences
Roles: Editor
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DOI: 10.1128/AEM.01738-20
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ABSTRACT

Prebiotics are increasingly examined for their ability to modulate the neonate gut microbiota of livestock, and products such as inulin are commonly added to milk replacer used in calving. However, the ability of specific members of the bovine neonate microbiota to respond to inulin remains to be determined, particularly among indigenous lactobacilli and bifidobacteria, beneficial genera commonly enriched by inulin. Screening of Bifidobacterium and Lactobacillus isolates obtained from fresh feces of dairy calves revealed that lactobacilli had a higher prevalence of inulin fermentation capacity (58%) than bifidobacteria (17%). Several Ligilactobacillus agilis (synonym Lactobacillus agilis) isolates exhibited vigorous growth on, and complete degradation of, inulin; however, the phenotype was strain specific. The most vigorous inulin-fermenting strain, L. agilis YZ050, readily degraded long-chain inulin not consumed by bifidobacterial isolates. Comparative genomic analysis of both L. agilis fermenter and nonfermenter strains indicated that strain YZ050 encodes an inulinase homolog, previously linked to extracellular degradation of long-chain inulin in Lacticaseibacillus paracasei, that was strongly induced during growth on inulin. Inulin catabolism by YZ050 also generates extracellular fructose, which can cross-feed other non-inulin-fermenting lactic acid bacteria isolated from the same bovine feces. The presence of specific inulin-responsive bacterial strains within calf gut microbiome provides a mechanistic rationale for enrichment of specific lactobacilli and creates a foundation for future synbiotic applications in dairy calves aimed at improving health in early life.

IMPORTANCE The gut microbiome plays an important role in animal health and is increasingly recognized as a target for diet-based manipulation. Inulin is a common prebiotic routinely added to animal feeds; however, the mechanism of inulin consumption by specific beneficial taxa in livestock is ill defined. In this study, we examined Lactobacillus and Bifidobacterium isolates from calves fed inulin-containing milk replacer and characterized specific strains that robustly consume long-chain inulin. In particular, novel Ligilactobacillus agilis strain YZ050 consumed inulin via an extracellular fructosidase, resulting in complete consumption of all long-chain inulin. Inulin catabolism resulted in temporal release of extracellular fructose, which can promote growth of other non-inulin-consuming strains of lactic acid bacteria. This work provides the mechanistic insight needed to purposely modulate the calf gut microbiome via the establishment of networks of beneficial microbes linked to specific prebiotics.

FOOTNOTES

    • Received 17 July 2020.
    • Accepted 30 September 2020.
    • Accepted manuscript posted online 2 October 2020.
  • Supplemental material is available online only.

  • Copyright © 2020 American Society for Microbiology.

All Rights Reserved.

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Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves
Yuanting Zhu, Jinxin Liu, Julian M. Lopez, David A. Mills
Applied and Environmental Microbiology Dec 2020, 87 (1) e01738-20; DOI: 10.1128/AEM.01738-20

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Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves
Yuanting Zhu, Jinxin Liu, Julian M. Lopez, David A. Mills
Applied and Environmental Microbiology Dec 2020, 87 (1) e01738-20; DOI: 10.1128/AEM.01738-20
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KEYWORDS

Ligilactobacillus agilis
inulin
bovine
synbiotic
exo-inulinase

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