Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Mathieu Almeida; Agnès Hébert; Anne-Laure Abraham; Simon Rasmussen; Christophe Monnet; Nicolas Pons; Céline Delbès; Valentin Loux; Jean-Michel Batto; Pierre Leonard; Sean Kennedy; Stanislas Dusko Ehrlich; Mihai Pop; Marie-Christine Montel; Françoise Irlinger; Pierre Renault

doi:10.1186/1471-2164-15-1101

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Mathieu Almeida, Agnès Hébert, Anne-Laure Abraham, Simon Rasmussen, Christophe Monnet, Nicolas Pons, Céline Delbès, Valentin Loux, Jean-Michel Batto, Pierre Leonard, Sean Kennedy, Stanislas Dusko Ehrlich, Mihai Pop, Marie-Christine Montel, Françoise Irlinger, Pierre Renault

41 Citations (Scopus)

Abstract

BACKGROUND: Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.

RESULTS: We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.

CONCLUSIONS: Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

Original language	English
Journal	BMC Genomics
Volume	15
Pages (from-to)	1101
ISSN	1471-2164
DOIs	https://doi.org/10.1186/1471-2164-15-1101
Publication status	Published - 13 Dec 2014
Externally published	Yes

Keywords

Bacteria/genetics
Cheese/microbiology
Dairy Products/microbiology
Databases, Genetic
Fermentation
Genome, Bacterial/genetics
Metagenomics/methods
Microbiota
Sequence Analysis

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1471-2164-15-1101Final published version, 1.33 MBLicence: CC BY

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Almeida, M., Hébert, A., Abraham, A.-L., Rasmussen, S., Monnet, C., Pons, N., Delbès, C., Loux, V., Batto, J.-M., Leonard, P., Kennedy, S., Ehrlich, S. D., Pop, M., Montel, M.-C., Irlinger, F., & Renault, P. (2014). Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics, 15, 1101. https://doi.org/10.1186/1471-2164-15-1101

Almeida, M, Hébert, A, Abraham, A-L, Rasmussen, S, Monnet, C, Pons, N, Delbès, C, Loux, V, Batto, J-M, Leonard, P, Kennedy, S, Ehrlich, SD, Pop, M, Montel, M-C, Irlinger, F & Renault, P 2014, 'Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products', BMC Genomics, vol. 15, pp. 1101. https://doi.org/10.1186/1471-2164-15-1101

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title = "Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products",

abstract = "BACKGROUND: Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.RESULTS: We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.CONCLUSIONS: Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.",

keywords = "Bacteria/genetics, Cheese/microbiology, Dairy Products/microbiology, Databases, Genetic, Fermentation, Genome, Bacterial/genetics, Metagenomics/methods, Microbiota, Sequence Analysis",

author = "Mathieu Almeida and Agn{\`e}s H{\'e}bert and Anne-Laure Abraham and Simon Rasmussen and Christophe Monnet and Nicolas Pons and C{\'e}line Delb{\`e}s and Valentin Loux and Jean-Michel Batto and Pierre Leonard and Sean Kennedy and Ehrlich, {Stanislas Dusko} and Mihai Pop and Marie-Christine Montel and Fran{\c c}oise Irlinger and Pierre Renault",

year = "2014",

month = dec,

day = "13",

doi = "10.1186/1471-2164-15-1101",

language = "English",

volume = "15",

pages = "1101",

journal = "BMC Genomics",

issn = "1471-2164",

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TY - JOUR

T1 - Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

AU - Almeida, Mathieu

AU - Hébert, Agnès

AU - Abraham, Anne-Laure

AU - Rasmussen, Simon

AU - Monnet, Christophe

AU - Pons, Nicolas

AU - Delbès, Céline

AU - Loux, Valentin

AU - Batto, Jean-Michel

AU - Leonard, Pierre

AU - Kennedy, Sean

AU - Ehrlich, Stanislas Dusko

AU - Pop, Mihai

AU - Montel, Marie-Christine

AU - Irlinger, Françoise

AU - Renault, Pierre

PY - 2014/12/13

Y1 - 2014/12/13

N2 - BACKGROUND: Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.RESULTS: We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.CONCLUSIONS: Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

AB - BACKGROUND: Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.RESULTS: We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.CONCLUSIONS: Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.

KW - Bacteria/genetics

KW - Cheese/microbiology

KW - Dairy Products/microbiology

KW - Databases, Genetic

KW - Fermentation

KW - Genome, Bacterial/genetics

KW - Metagenomics/methods

KW - Microbiota

KW - Sequence Analysis

U2 - 10.1186/1471-2164-15-1101

DO - 10.1186/1471-2164-15-1101

M3 - Journal article

C2 - 25496341

SN - 1471-2164

VL - 15

SP - 1101

JO - BMC Genomics

JF - BMC Genomics

ER -

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products

Abstract

Keywords

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