Isolation and Comparative Genomic Analysis of Reuterin-Producing Lactobacillus reuteri From the Chicken Gastrointestinal Tract.
Identifieur interne : 000025 ( Main/Exploration ); précédent : 000024; suivant : 000026Isolation and Comparative Genomic Analysis of Reuterin-Producing Lactobacillus reuteri From the Chicken Gastrointestinal Tract.
Auteurs : Anna Greppi [Suisse] ; Paul T. Asare [Suisse] ; Clarissa Schwab [Suisse] ; Niklaus Zemp [Suisse] ; Roger Stephan [Suisse] ; Christophe Lacroix [Suisse]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2020.
Abstract
Lactobacillus reuteri is a natural inhabitant of selected animal and human gastrointestinal tract (GIT). Certain strains have the capacity to transform glycerol to 3-hydroxypropionaldehyde (3-HPA), further excreted to form reuterin, a potent antimicrobial system. Reuterin-producing strains may be applied as a natural antimicrobial in feed to prevent pathogen colonization of animals, such as in chicken, and replace added antimicrobials. To date, only seven L. reuteri strains isolated from chicken have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate L. reuteri strains from chicken GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy strains were isolated from faces, crops and ceca of six chicken from poultry farms and samples from slaughterhouse. Twenty-five strains were selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated into a phylogenetic tree of 40 strains from different hosts. Phylogenetic analysis based on gene content as well as on core genomes showed grouping of the selected 25 L. reuteri chicken isolates within the poultry/human lineage VI. Strains harboring pdu-cob-cbi-hem genes (23/25) produced between 156 mM ± 11 and 330 mM ± 14 3-HPA, from 600 mM of glycerol, in the conditions of the test. All 25 chicken strains were sensitive to cefotaxime (MIC between 0.016 and 1 μg/mL) and penicillin (MIC between 0.02 and 4 μg/mL). Akin to the reference strains DSM20016 and SD2112, the novel isolates were resistant to penicillin, possibly associated with identified point mutations in ponA, pbpX, pbpF and pbpB. All strains resistant to erythromycin (4/27) carried the ermB gene, and it was only present in chicken strains. All strains resistant to tetracycline (5/27) harbored tetW gene. This study confirms the evolutionary history of poultry/human lineage VI and identifies pdu-cob-cbi-hem as a frequent trait but not always present in this lineage. L. reuteri chicken strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of chicken.
DOI: 10.3389/fmicb.2020.01166
PubMed: 32670217
PubMed Central: PMC7326114
Affiliations:
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Asare</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich</wicri:regionArea><wicri:noRegion>Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Schwab, Clarissa" sort="Schwab, Clarissa" uniqKey="Schwab C" first="Clarissa" last="Schwab">Clarissa Schwab</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich</wicri:regionArea><wicri:noRegion>Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Zemp, Niklaus" sort="Zemp, Niklaus" uniqKey="Zemp N" first="Niklaus" last="Zemp">Niklaus Zemp</name><affiliation wicri:level="1"><nlm:affiliation>Genetic Diversity Centre, Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Genetic Diversity Centre, Department of Environmental Systems Sciences, ETH Zurich, Zurich</wicri:regionArea><wicri:noRegion>Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Stephan, Roger" sort="Stephan, Roger" uniqKey="Stephan R" first="Roger" last="Stephan">Roger Stephan</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute for Food Safety and Hygiene, University of Zurich, Zurich</wicri:regionArea><orgName type="university">Université de Zurich</orgName><placeName><settlement type="city">Zurich</settlement><region nuts="3" type="region">Canton de Zurich</region></placeName></affiliation></author><author><name sortKey="Lacroix, Christophe" sort="Lacroix, Christophe" uniqKey="Lacroix C" first="Christophe" last="Lacroix">Christophe Lacroix</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich</wicri:regionArea><wicri:noRegion>Zurich</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Lactobacillus reuteri</i> is a natural inhabitant of selected animal and human gastrointestinal tract (GIT). Certain strains have the capacity to transform glycerol to 3-hydroxypropionaldehyde (3-HPA), further excreted to form reuterin, a potent antimicrobial system. Reuterin-producing strains may be applied as a natural antimicrobial in feed to prevent pathogen colonization of animals, such as in chicken, and replace added antimicrobials. To date, only seven <i>L. reuteri</i> strains isolated from chicken have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate <i>L. reuteri</i> strains from chicken GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy strains were isolated from faces, crops and ceca of six chicken from poultry farms and samples from slaughterhouse. Twenty-five strains were selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated into a phylogenetic tree of 40 strains from different hosts. Phylogenetic analysis based on gene content as well as on core genomes showed grouping of the selected 25 <i>L. reuteri</i> chicken isolates within the poultry/human lineage VI. Strains harboring <i>pdu-cob-cbi-hem</i> genes (23/25) produced between 156 mM ± 11 and 330 mM ± 14 3-HPA, from 600 mM of glycerol, in the conditions of the test. All 25 chicken strains were sensitive to cefotaxime (MIC between 0.016 and 1 μg/mL) and penicillin (MIC between 0.02 and 4 μg/mL). Akin to the reference strains DSM20016 and SD2112, the novel isolates were resistant to penicillin, possibly associated with identified point mutations in <i>ponA</i>, <i>pbpX</i>, <i>pbpF</i> and <i>pbpB</i>. All strains resistant to erythromycin (4/27) carried the <i>ermB</i> gene, and it was only present in chicken strains. All strains resistant to tetracycline (5/27) harbored <i>tetW</i> gene. This study confirms the evolutionary history of poultry/human lineage VI and identifies <i>pdu-cob-cbi-hem</i> as a frequent trait but not always present in this lineage. <i>L. reuteri</i> chicken strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of chicken.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32670217</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>28</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><PubDate><Year>2020</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>Isolation and Comparative Genomic Analysis of Reuterin-Producing <i>Lactobacillus reuteri</i> From the Chicken Gastrointestinal Tract.</ArticleTitle><Pagination><MedlinePgn>1166</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2020.01166</ELocationID><Abstract><AbstractText><i>Lactobacillus reuteri</i> is a natural inhabitant of selected animal and human gastrointestinal tract (GIT). Certain strains have the capacity to transform glycerol to 3-hydroxypropionaldehyde (3-HPA), further excreted to form reuterin, a potent antimicrobial system. Reuterin-producing strains may be applied as a natural antimicrobial in feed to prevent pathogen colonization of animals, such as in chicken, and replace added antimicrobials. To date, only seven <i>L. reuteri</i> strains isolated from chicken have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate <i>L. reuteri</i> strains from chicken GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy strains were isolated from faces, crops and ceca of six chicken from poultry farms and samples from slaughterhouse. Twenty-five strains were selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated into a phylogenetic tree of 40 strains from different hosts. Phylogenetic analysis based on gene content as well as on core genomes showed grouping of the selected 25 <i>L. reuteri</i> chicken isolates within the poultry/human lineage VI. Strains harboring <i>pdu-cob-cbi-hem</i> genes (23/25) produced between 156 mM ± 11 and 330 mM ± 14 3-HPA, from 600 mM of glycerol, in the conditions of the test. All 25 chicken strains were sensitive to cefotaxime (MIC between 0.016 and 1 μg/mL) and penicillin (MIC between 0.02 and 4 μg/mL). Akin to the reference strains DSM20016 and SD2112, the novel isolates were resistant to penicillin, possibly associated with identified point mutations in <i>ponA</i>, <i>pbpX</i>, <i>pbpF</i> and <i>pbpB</i>. All strains resistant to erythromycin (4/27) carried the <i>ermB</i> gene, and it was only present in chicken strains. All strains resistant to tetracycline (5/27) harbored <i>tetW</i> gene. This study confirms the evolutionary history of poultry/human lineage VI and identifies <i>pdu-cob-cbi-hem</i> as a frequent trait but not always present in this lineage. <i>L. reuteri</i> chicken strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of chicken.</AbstractText><CopyrightInformation>Copyright © 2020 Greppi, Asare, Schwab, Zemp, Stephan and Lacroix.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Greppi</LastName><ForeName>Anna</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Asare</LastName><ForeName>Paul T</ForeName><Initials>PT</Initials><AffiliationInfo><Affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schwab</LastName><ForeName>Clarissa</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zemp</LastName><ForeName>Niklaus</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Genetic Diversity Centre, Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stephan</LastName><ForeName>Roger</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lacroix</LastName><ForeName>Christophe</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Food, Nutrition and Health, Laboratory of Food Biotechnology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>06</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Lactobacillus reuteri</Keyword><Keyword MajorTopicYN="N">antimicrobial</Keyword><Keyword MajorTopicYN="N">chicken</Keyword><Keyword MajorTopicYN="N">comparative genomics</Keyword><Keyword 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Asare</name><name sortKey="Lacroix, Christophe" sort="Lacroix, Christophe" uniqKey="Lacroix C" first="Christophe" last="Lacroix">Christophe Lacroix</name><name sortKey="Schwab, Clarissa" sort="Schwab, Clarissa" uniqKey="Schwab C" first="Clarissa" last="Schwab">Clarissa Schwab</name><name sortKey="Stephan, Roger" sort="Stephan, Roger" uniqKey="Stephan R" first="Roger" last="Stephan">Roger Stephan</name><name sortKey="Zemp, Niklaus" sort="Zemp, Niklaus" uniqKey="Zemp N" first="Niklaus" last="Zemp">Niklaus Zemp</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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