Comparative genomics of the lactic acid bacteria
Kira S. Makarova,Alexei I. Slesarev,Yuri I. Wolf,Alexander V. Sorokin,Boris Mirkin,Eugene V. Koonin,Andrey R. Pavlov,Nadezhda Pavlova,Valeri N. Karamychev,N. N. Polouchine,V. V. Shakhova,Igor V. Grigoriev,Yunian Lou,D. Rohksar,Susan Lucas,Katherine H. Huang,David Goodstein,Trevor Hawkins,V. Plengvidhya,V. Plengvidhya,Dennis L. Welker,Joanne E. Hughes,Yong Jun Goh,Andrew K. Benson,K. A. Baldwin,Ju-Hoon Lee,I. Diaz-Muniz,B. Dosti,Vladimir V. Smeianov,W. Wechter,Ravi D. Barabote,Graciela L. Lorca,Eric Altermann,Rodolphe Barrangou,Balasubramanian Ganesan,Y. Xie,Helen Rawsthorne,Diana I. Tamir,C. Parker,Frederick Breidt,Frederick Breidt,Jeffery R. Broadbent,Robert W. Hutkins,Daniel J. O'Sullivan,J. L. Steele,Gülhan Ünlü,Milton H. Saier,Todd R. Klaenhammer,Paul G. Richardson,Sergei A. Kozyavkin,Bart C. Weimer,David A. Mills +51 more
TLDR
Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.Abstract:
Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.read more
Citations
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Phage response to CRISPR-encoded resistance in Streptococcus thermophilus.
Hélène Deveau,Rodolphe Barrangou,Josiane E. Garneau,Jessica M. Labonté,Christophe Fremaux,Patrick Boyaval,Dennis A. Romero,Philippe Horvath,Sylvain Moineau +8 more
TL;DR: It is shown through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.
Journal ArticleDOI
Expanded microbial genome coverage and improved protein family annotation in the COG database
TL;DR: An update of the Clusters of Orthologous Groups of proteins, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level are presented.
Journal ArticleDOI
Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus
Philippe Horvath,Dennis A. Romero,Anne Claire Coûté-Monvoisin,Melissa Richards,Hélène Deveau,Sylvain Moineau,Patrick Boyaval,Christophe Fremaux,Rodolphe Barrangou +8 more
TL;DR: A novel Streptococcus thermophilus locus is characterized, and its ability to integrate novel spacers in response to bacteriophage is experimentally demonstrated, and it is hypothesized that the level of diversity is correlated with relative CRISPR activity and proposed that the activity is highest for CRISpr1, followed by CRIS PR3, while CRISP2 may be degenerate.
Journal ArticleDOI
Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein
Matti Kankainen,Lars Paulin,Soile Tynkkynen,Ingemar von Ossowski,Justus Reunanen,Pasi Partanen,Reetta Satokari,Satu Vesterlund,Antoni P. A. Hendrickx,Sarah Lebeer,Sigrid C. J. De Keersmaecker,Jos Vanderleyden,Tuula Hämäläinen,Suvi Laukkanen,Noora Salovuori,Jarmo Ritari,Edward Alatalo,Riitta Korpela,Tiina Mattila-Sandholm,Anna Lassig,Katja Hatakka,Katri T. Kinnunen,Heli Karjalainen,Maija Saxelin,Kati Laakso,Anu Surakka,Airi Palva,Tuomas Salusjärvi,Petri Auvinen,Willem M. de Vos +29 more
TL;DR: It is concluded that the presence of SpaC is essential for the mucus interaction of L. rhamnosus GG and likely explains its ability to persist in the human intestinal tract longer than LC705 during an intervention trial.
Journal ArticleDOI
Microorganisms with claimed probiotic properties: an overview of recent literature.
TL;DR: Caution in selecting and monitoring of probiotics for patients is needed and complete consideration of risk-benefit ratio before prescribing is recommended, as probiotic properties have been shown to be strain specific, accurate identification of particular strains is also very important.
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