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

BMC Genomics

Pierre Renault⁷  Françoise Irlinger⁵  Marie-Christine Montel³  Mihai Pop²  Stanislas Dusko Ehrlich⁶  Sean Kennedy⁶  Pierre Leonard⁶  Jean-Michel Batto⁶  Valentin Loux⁸  Céline Delbès³  Nicolas Pons⁶  Christophe Monnet⁵  Simon Rasmussen⁴  Anne-Laure Abraham⁷  Agnès Hébert¹  Mathieu Almeida² 

[1] AgroParisTech, UMR 782 GMPA, 78850 Thiverval-Grignon, France;Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA;Institut National de la Recherche Agronomique, UR 545 URF, 15000 Aurillac, France;Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark;Institut National de la Recherche Agronomique, UMR 782 GMPA, 78850 Thiverval-Grignon, France;Institut National de la Recherche Agronomique, US 1367 MGP, 78352 Jouy-en-Josas, France;AgroParisTech, UMR MICALIS, 78352 Jouy-en-Josas, France;Institut National de la Recherche Agronomique, UR 1077 MIG, 78352 Jouy-en-Josas, France

关键词: Dairy ecosystems;    Food bacteria;    Metagenomics;    Comparative genomics;    Next-generation sequencing;    Sequence assembly;    Genome sequencing;    Genomic libraries;   

Others  :  1127351
DOI  :  10.1186/1471-2164-15-1101

 received in 2014-06-20, accepted in 2014-12-04,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Almeida et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Feurer C, Irlinger F, Spinnler HE, Glaser P, Vallaeys T: Assessment of the rind microbial diversity in a farmhouse-produced vs a pasteurized industrially produced soft red-smear cheese using both cultivation and rDNA-based methods. J Appl Microbiol 2004, 97:546-556.
• [2]Rea MC, Görges S, Gelsomino R, Brennan NM, Mounier J, Vancanneyt M, Scherer S, Swings J, Cogan TM: Stability of the biodiversity of the surface consortia of Gubbeen, a red-smear cheese. J Dairy Sci 2007, 90:2200-2210.
• [3]Goerges S, Mounier J, Rea MC, Gelsomino R, Heise V, Beduhn R, Cogan TM, Vancanneyt M, Scherer S: Commercial ripening starter microorganisms inoculated into cheese milk do not successfully establish themselves in the resident microbial ripening consortia of a South German red smear cheese. Appl Environ Microbiol 2008, 74:2210-2217.
• [4]Larpin-Laborde S, Imran M: Surface microbial consortia from Livarot, a French smear-ripened cheese. Can J Microbiol 2011, 660:651-660.
• [5]Feutry F, Oneca M, Berthier F, Torre P: Biodiversity and growth dynamics of lactic acid bacteria in artisanal PDO Ossau-Iraty cheeses made from raw ewe’s milk with different starters. Food Microbiol 2012, 29:33-42.
• [6]Montel MC, Buchin S, Mallet A, Delbes-Paus C, Vuitton DA, Desmasures N, Berthier F: Traditional cheeses: rich and diverse microbiota with associated benefits. Int J Food Microbiol 2014, 177:136-154.
• [7]Delbès C, Ali-Mandjee L, Montel M-C: Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl Environ Microbiol 2007, 73:1882-1891.
• [8]Feurer C, Vallaeys T, Corrieu G, Irlinger F: Does smearing inoculum reflect the bacterial composition of the smear at the end of the ripening of a French soft, red-smear cheese? J Dairy Sci 2004, 87:3189-3197.
• [9]Mounier J, Monnet C, Jacques N, Antoinette A, Irlinger F: Assessment of the microbial diversity at the surface of Livarot cheese using culture-dependent and independent approaches. Int J Food Microbiol 2009, 133:31-37.
• [10]Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML, Hammes WP, Harnett J, Huys G, Laulund S, Ouwehand A, Powell IB, Prajapati JB, Seto Y, Ter Schure E, Van Boven A, Vankerckhoven V, Zgoda A, Tuijtelaars S, Hansen EB: Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol 2012, 154:87-97.
• [11]Roth E, Miescher Schwenninger S, Hasler M, Eugster-Meier E, Lacroix C: Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis. BMC Microbiol 2010, 10:74. BioMed Central Full Text
• [12]Ishikawa M, Kodama K, Yasuda H, Okamoto-Kainuma A, Koizumi K, Yamasato K: Presence of halophilic and alkaliphilic lactic acid bacteria in various cheeses. Lett Appl Microbiol 2007, 44:308-313.
• [13]Masoud W, Vogensen FK, Lillevang S, Abu Al-Soud W, Sørensen SJ, Jakobsen M: The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR. Int J Food Microbiol 2012, 153:192-202.
• [14]Brennan NM, Brown R, Goodfellow M, Ward AC, Beresford TP, Vancanneyt M, Cogan TM, Fox PF: Microbacterium gubbeenense sp. nov., from the surface of a smear-ripened cheese. Int J Syst Evol Microbiol 2001, 51(Pt 6):1969-1976.
• [15]Irlinger F, Bimet F, Delettre J, Lefèvre M, Grimont PAD: Arthrobacter bergerei sp. nov. and Arthrobacter arilaitensis sp. nov., novel coryneform species isolated from the surfaces of cheeses. Int J Syst Evol Microbiol 2005, 55(Pt 1):457-462.
• [16]Bora N, Vancanneyt M, Gelsomino R, Swings J, Brennan N, Cogan TM, Larpin S, Desmasures N, Lechner FE, Kroppenstedt RM, Ward AC, Goodfellow M: Agrococcus casei sp. nov., isolated from the surfaces of smear-ripened cheeses. Int J Syst Evol Microbiol 2007, 57(Pt 1):92-97.
• [17]Bleicher A, Neuhaus K, Scherer S: Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses. Int J Syst Evol Microbiol 2010, 60(Pt 8):1745-1749.
• [18]Didienne R, Defargues C, Callon C, Meylheuc T, Hulin S, Montel M-C: Characteristics of microbial biofilm on wooden vats (’gerles’) in PDO Salers cheese. Int J Food Microbiol 2012, 156:91-101.
• [19]Verdier-Metz I, Gagne G, Bornes S, Monsallier F, Veisseire P, Delbès-Paus C, Montel M-C: Cow teat skin, a potential source of diverse microbial populations for cheese production. Appl Environ Microbiol 2012, 78:326-333.
• [20]Monnet C, Loux V, Gibrat J-F, Spinnler E, Barbe V, Vacherie B, Gavory F, Gourbeyre E, Siguier P, Chandler M, Elleuch R, Irlinger F, Vallaeys T: The Arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese. PLoS One 2010, 5:14.
• [21]Falentin H, Deutsch S-M, Jan G, Loux V, Thierry A, Parayre S, Maillard M-B, Dherbécourt J, Cousin FJ, Jardin J, Siguier P, Couloux A, Barbe V, Vacherie B, Wincker P, Gibrat J-F, Gaillardin C, Lortal S: The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PLoS One 2010, 5:e11748.
• [22]Schröder J, Maus I, Trost E, Tauch A: Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation. BMC Genomics 2011, 12:545. BioMed Central Full Text
• [23]Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A, Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Diaz-Muniz I, Dosti B, Smeianov V, Wechter W, Barabote R, et al.: Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 2006.
• [24]Sjöling S, Cowan D: Metagenomics: microbial community genomes revealed. Psychrophiles from Biodivers to Biotechnol 2008, 313-332.
• [25]Kullen MJ, Sanozky-Dawes RB, Crowell DC, Klaenhammer TR: Use of the DNA sequence of variable regions of the 16S rRNA gene for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. J Appl Microbiol 2000, 89:511-516.
• [26]Ercolini D: High-throughput sequencing and metagenomics: steps ahead in the culture-independent analysis of food microbial ecology. Appl Environ Microbiol 2013.
• [27]Ercolini D: High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl Environ Microbiol 2013, 79:3148-3155.
• [28]Bokulich NA, Mills DA: Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants. Appl Environ Microbiol 2013, 79:5214-5223.
• [29]Lusk TS, Ottesen AR, White JR, Allard MW, Brown EW, Kase JA: Characterization of microflora in Latin-style cheeses by next-generation sequencing technology. BMC Microbiol 2012, 12:254. BioMed Central Full Text
• [30]Ercolini D, De Filippis F, La Storia A, Iacono M: “Remake” by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl Environ Microbiol 2012, 78:8142-8145.
• [31]Quigley L, O’Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD: High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ Microbiol 2012, 78:5717-5723.
• [32]Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C: Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 2012, 8:e1002358.
• [33]Wolfe BE, Button JE, Santarelli M, Dutton RJ: Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 2014, 158:422-433.
• [34]Huson D, Mitra S, Ruscheweyh H: Integrative analysis of environmental sequences using MEGAN4. Genome Res 2011, 21:1552-1560.
• [35]Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto J-M, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, et al.: Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 2014, 32:822-828.
• [36]Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto J-M, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, et al.: Richness of human gut microbiome correlates with metabolic markers. Nature 2013, 500:541-546.
• [37]Altschul S, Gish W, Miller W: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
• [38]Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Human Microbiome Jumpstart Reference Strains Consortium, et al.: A catalog of reference genomes from the human microbiome. Science 2010, 328(5981):994-999.
• [39]Callister SJ, McCue LA, Turse JE, Monroe ME, Auberry KJ, Smith RD, Adkins JN, Lipton MS: Comparative bacterial proteomics: analysis of the core genome concept. PLoS One 2008, 3:e1542.
• [40]Mende DR, Sunagawa S, Zeller G, Bork P: Accurate and universal delineation of prokaryotic species. Nat Methods 2013, 10:881-884.
• [41]Crocker FH, Fredrickson JK, White DC, Ringelberg DB, Balkwill DL: Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments. Microbiology 2000, 146(Pt 6):1295-1310.
• [42]Jans C, Follador R, Hochstrasser M, Lacroix C, Meile L, Stevens MJA: Comparative genome analysis of Streptococcus infantarius subsp. infantarius CJ18, an African fermented camel milk isolate with adaptations to dairy environment. BMC Genomics 2013, 14:200. BioMed Central Full Text
• [43]Jans C, Gerber A, Bugnard J, Njage PMK, Lacroix C, Meile L: Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus. Food Microbiol 2012, 31:33-42.
• [44]Csurös M, Milosavljevic A: Pooled genomic indexing (PGI): analysis and design of experiments. J Comput Biol 2004, 11:1001-1021.
• [45]Aird D, Ross MG, Chen W-S, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011, 12:R18. BioMed Central Full Text
• [46]Vianna PCB, Mazal G, Santos MV, Bolini HMA, Gigante ML: Microbial and sensory changes throughout the ripening of Prato cheese made from milk with different levels of somatic cells. J Dairy Sci 2008, 91:1743-1750.
• [47]Jaeggi JJ, Govindasamy-Lucey S, Berger YM, Johnson ME, McKusick BC, Thomas DL, Wendorff WL: Hard ewe’s milk cheese manufactured from milk of three different groups of somatic cell counts. J Dairy Sci 2003, 86:3082-3089.
• [48]Meslier V, Loux V, Renault P: Genome sequence of Leuconostoc pseudomesenteroides strain 4882, isolated from a dairy starter culture. J Bacteriol 2012, 194:6637.
• [49]Maoz A, Mayr R, Scherer S: Temporal stability and biodiversity of two complex antilisterial cheese-ripening microbial consortia. Appl Environ Microbiol 2003, 69:4012-4018.
• [50]Ogier J, Lafarge V, Girard V: Molecular fingerprinting of dairy microbial ecosystems by use of temporal temperature and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2004, 70:5628-5643.
• [51]Fontana C, Cappa F, Rebecchi A, Cocconcelli PS: Surface microbiota analysis of Taleggio, Gorgonzola, Casera, Scimudin and Formaggio di Fossa Italian cheeses. Int J Food Microbiol 2010, 138:205-211.
• [52]Bockelmann W, Willems KP, Neve H, Heller KH: Cultures for the ripening of smear cheeses. Int Dairy J 2005, 15:719-732.
• [53]Mounier J, Gelsomino R: Surface microflora of four smear-ripened cheeses. Appl Env Microbiol 2005, 71:6489-6500.
• [54]Edwards U, Rogall T, Blöcker H: Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989, 17:7843-7853.
• [55]Adékambi T, Drancourt M, Raoult D: The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 2009, 17:37-45.
• [56]Tayeb LA, Lefevre M, Passet V, Diancourt L, Brisse S, Grimont PAD: Comparative phylogenies of Burkholderia, Ralstonia, Comamonas, Brevundimonas and related organisms derived from rpoB, gyrB and rrs gene sequences. Res Microbiol 2008, 159:169-177.
• [57]Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877.
• [58]Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012, 1:18. BioMed Central Full Text
• [59]McCallum A, Nigam K, Ungar L: Efficient Clustering of High-Dimensional Data Sets With Application to Reference Matching. 2000, 169-178. [Proceedings of the sixth ACM SIGKDD international conference on Knowledge discovery and data mining]
• [60]Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. BioMed Central Full Text
• [61]Li H, Durbin R: Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 2009, 25:1754-1760.
• [62]Kelley D, Schatz M, Salzberg S: Quake: quality-aware detection and correction of sequencing errors. Genome Biol 2010, 11:R116. BioMed Central Full Text
• [63]Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
• [64]Chain P, Grafham D, Fulton R: Genome project standards in a new era of sequencing. Science 2009, 326(5950):236-237.
• [65]Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. BioMed Central Full Text
• [66]Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797.
• [67]Price M, Dehal P, Arkin A: FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5:e9490.
• [68]Letunic I, Bork P: Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 2011, 39:W475-W478.