Complete Chromosome Sequence of Carnobacterium maltaromaticum LMA 28

Within the lactic acid bacterium genus Carnobacterium, Carnobacterium maltaromaticum is one of the most frequently isolated species from natural environments and food. It potentially plays a major role in food product biopreservation. We report here on the 3.649-Mb chromosome sequence of C. maltaromaticum LMA 28, which was isolated from ripened soft cheese

Unique β-Glucuronidase Locus in Gut Microbiomes of Crohn's Disease Patients and Unaffected First-Degree Relatives.

Crohn's disease, an incurable chronic inflammatory bowel disease, has been attributed to both genetic predisposition and environmental factors. A dysbiosis of the gut microbiota, observed in numerous patients but also in at least one hundred unaffected first-degree relatives, was proposed to have a causal role. Gut microbiota β-D-glucuronidases (EC 3.2.1.33) hydrolyse β-D-glucuronate from glucuronidated compounds. They include a GUS group, that is homologous to the Escherichia coli GusA, and a BG group, that is homologous to metagenomically identified H11G11 BG and has unidentified natural substrates. H11G11 BG is part of the functional core of the human gut microbiota whereas GusA, known to regenerate various toxic products, is variably found in human subjects. We investigated potential risk markers for Crohn's disease using DNA-sequence-based exploration of the β-D-glucuronidase loci (GUS or Firmicute H11G11-BG and the respective co-encoded glucuronide transporters). Crohn's disease-related microbiomes revealed a higher frequency of a C7D2 glucuronide transporter (12/13) compared to unrelated healthy subjects (8/32). This transporter was in synteny with the potential harmful GUS β-D-glucuronidase as only observed in a Eubacterium eligens plasmid. A conserved NH2-terminal sequence in the transporter (FGDFGND motif) was found in 83% of the disease-related subjects and only in 12% of controls. We propose a microbiota-pathology hypothesis in which the presence of this unique β-glucuronidase locus may contribute to an increase risk for Crohn's disease

Gene neighborhood views of H11G1 and C7D2 transporters loci.

<p>We analyzed genes that co-localized with C7D2 or H11G11 transporters from groups 1, 2 and 5 as previously defined (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148291#pone.0148291.g002" target="_blank">Fig 2</a>). Gene neighborhood views from microbiomes were obtained using the Gene Mark prediction tool and annotated published genomes. Red box, glucuronide transporter; blue box, BG or GUS β-glucuronidases; black box, AraC family transcriptional regulator; brown box, putative esterase lipase; empty box, putative protein; slashes, sequence end. Homologous sequences are surrounded by same color lines. *: CD patient. Spanish subjects are underlined. This analysis of genes neighboring H11G11 and C7D2 transporters reveals that most CDR have an unexpected C7D2 transporter/GUS β-glucuronidase locus.</p

Phylogenetic tree of H11G11 and C7D2 transporters in CDR and CDU microbiomes.

<p>Analysis was performed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148291#pone.0148291.g001" target="_blank">Fig 1</a>. Twenty nine protein sequences were retained (>30% identity, > 80% coverage) from the best Blast results for each query. The phylogenetic assignments were performed by searching homologs in published genomes (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148291#pone.0148291.s011" target="_blank">S3 Table</a>). All protein sequences were aligned using Expresso (3D Coffee) and a Neighbor-Joining tree was performed using MEGA 5.5. Groups are proposed for clusters within high identity percentages (>42% within each group). Sequence names are referred to as: query used/ microbiome sequence name (Metahit and ID 28117 projects). Black and white symbols are used to distinguish CD-related subjects (patients and asymptomatic first-degree relatives; CDR) and CD-unrelated healthy subjects, respectively. The queries used (H11G11 and C7D2 transporters) are underlined. Squares and circles correspond to results using respectively H11G11 and C7D2 transporters as query. This <i>in silico</i> exploration of CDR and CDU microbiomes reveals that H11G11 transporter is mostly present in healthy subjects, whereas C7D2 transporter is recovered in CDR subjects, including unaffected relatives. The C7D2 transporter is plasmid-encoded or present on specific Clostridiale chromosomes.</p

A conserved NH2-terminal motif in C7D2 transporters from CD related microbiomes.

<p><b>(A)</b> Alignment of NH2-terminal motifs from H11G11 and C7D2 transporters. NH2 terminal motifs were extracted from Expresso (3D Coffee) alignment performed from H11G11 and C7D2 transporters sequences presented <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148291#pone.0148291.g001" target="_blank">Fig 1</a>. * CD unrelated healthy subjects with C7D2 transporter, † no ORF predicted. Black squares indicate C7D2 transporter from CD related microbiomes. Spanish subjects are underlined. <b>(B)</b> Phylogenetic tree based on an alignment restricted to the “FGDFGND” NH2-terminal motif. Neighbor-Joining method was used to perform the tree. Sequences from F1S and C7D2 are absent because the first has no predicted ORF and the second has a truncated NH2-terminal sequence. <b>(C)</b> Proposed pattern for a beta-glucuronidase linked transporter specific of CD related microbiomes. The conserved pattern was determined using C7D2 transporter sequences from CD related microbiomes and published genomes (carrying GND-end motif) as found by the pattern discovery tool PRATT (<a href="http://www.expasy.ch/tools/pratt/" target="_blank">http://www.expasy.ch/tools/pratt/</a>).</p

The genetics of microbial starters

The main bacterial species used in meat fermentation are lactic acid bacteria and coagulase-negative staphylococci. Genetic studies have provided basic knowledge on their metabolic activities and their fitness in meat products. The genome sequences of several starter strains have confirmed their role in the development of the sensorial properties of fermented sausages but have also revealed the main functions characterizing their resistance to stressful environmental conditions encountered during sausage manufacturing. Comparative genomics studies have allowed estimation of the core genomes and the flexible gene pools within the main species. Plasmid sequences from different lactic acid bacteria are available and reveal that some technological traits are associated to plasmidic genes. Appropriate genetic tools for molecular genetic analyses have also been developed, allowing the exchange of chromosomal genes or plasmids. Post-genomic studies using different approaches such as proteomics and transcriptomics have revealed the potentialities of the main starter cultures

(p)ppGpp/GTP and Malonyl-CoA Modulate Staphylococcus aureus Adaptation to FASII Antibiotics and Provide a Basis for Synergistic Bi-Therapy

International audienceFatty acid biosynthesis (FASII) enzymes are considered valid targets for antimicrobial drug development against the human pathogen Staphylococcus aureus. However, incorporation of host fatty acids confers FASII antibiotic adaptation that compromises prospective treatments. S. aureus adapts to FASII inhibitors by first entering a nonreplicative latency period, followed by outgrowth. Here, we used transcriptional fusions and direct metabolite measurements to investigate the factors that dictate the duration of latency prior to outgrowth. We show that stringent response induction leads to repression of FASII and phospholipid synthesis genes. (p)ppGpp induction inhibits synthesis of malonyl-CoA, a molecule that derepresses FapR, a key regulator of FASII and phospholipid synthesis. Anti-FASII treatment also triggers transient expression of (p)ppGpp-regulated genes during the anti-FASII latency phase, with concomitant repression of FapR regulon expression. These effects are reversed upon outgrowth. GTP depletion, a known consequence of the stringent response, also occurs during FASII latency, and is proposed as the common signal linking these responses. We next showed that anti-FASII treatment shifts malonyl-CoA distribution between its interactants FapR and FabD, toward FapR, increasing expression of the phospholipid synthesis genes plsX and plsC during outgrowth. We conclude that components of the stringent response dictate malonyl-CoA availability in S. aureus FASII regulation, and contribute to latency prior to anti-FASII-adapted outgrowth. A combinatory approach, coupling a (p)ppGpp inducer and an anti-FASII, blocks S. aureus outgrowth, opening perspectives for bi-therapy treatmen