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1.  New Microbes New Infections promotes modern prokaryotic taxonomy: a new section “TaxonoGenomics: new genomes of microorganisms in humans” 
doi:10.1016/j.nmni.2015.06.001
PMCID: PMC4506979  PMID: 26199732
Clinical microbiology; genomics; MALDI-TOF; taxono-genomics; taxonomy
2.  ‘Clostridium massiliodielmoense’, a new species isolated from the human gut microbiota 
Herein, we report the main characteristics of ‘Clostridium massiliodielmoense’ strain mt26 (= CSUR P2255), representative of a new species isolated from the gastrointestinal tract of a healthy 28-month-old Senegalese boy.
doi:10.1016/j.nmni.2016.05.014
PMCID: PMC4919720  PMID: 27366325
“Clostridium massiliodielmoense’; culturomics; gut microbiota; taxono-genomics
3.  Prospective Comparison of Infective Endocarditis in Khon Kaen, Thailand and Rennes, France 
Prospectively collected, contemporary data are lacking on how the features of infective endocarditis (IE) vary according to region. We, therefore, compared IE in Rennes, France and Khon Kaen, Thailand. Fifty-eight patients with confirmed IE were enrolled at each site during 2011 and 2012 using a common protocol. Compared with French patients, Thais had a lower median age (47 versus 70 years old; P < 0.001) and reported more animal contact (86% versus 21%; P < 0.001). There were more zoonotic infections among Thai than France patients (6 and 1 cases; P = 0.017) and fewer staphylococcal infections (4 versus 15 cases; P = 0.011). Underlying rheumatic heart disease was more prevalent in Thai than in French patients (31% and 4%; P = 0.001), whereas prosthetic heart valves were less prevalent (9% and 35%; P = 0.001). Our data strengthen previous observations that IE in the tropics has distinctive demographic characteristics, risk factors, and etiologies and underscore the need for improved prevention and control strategies.
doi:10.4269/ajtmh.14-0689
PMCID: PMC4385788  PMID: 25646262
4.  Draft Genome Sequence of Actinobaculum massiliense Strain FC3 
Genome Announcements  2016;4(1):e01537-15.
Actinobaculum massiliense strain FC3 was isolated from the urine of a patient with acute cystitis. The 2.06-Mb genome of strain FC3 contains 17 toxin/antitoxin modules and 9 bacteriocin-encoding genes that may play a role in virulence. The genome also exhibits 693 genes acquired by lateral gene transfer.
doi:10.1128/genomeA.01537-15
PMCID: PMC4714112  PMID: 26769930
5.  Genome Sequence of Bacillus simplex Strain P558, Isolated from a Human Fecal Sample 
Genome Announcements  2014;2(6):e01241-14.
Bacillus simplex strain P558 was isolated from a fecal sample of a 25-year-old Saudi male. We sequenced the 5.98-Mb genome of the strain and compared it to that of B. simplex strain 1NLA3E.
doi:10.1128/genomeA.01241-14
PMCID: PMC4263825  PMID: 25502663
6.  Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium 
Genome Announcements  2014;2(6):e01171-14.
Rickettsia hoogstraalii is a tick-associated member of the spotted fever group rickettsiae that is geographically widely distributed. We report here the draft genome of R. hoogstraalii strain CroaticaT (=DSM 22243 = UTMB 00003), which was isolated from Haemaphysalis sulcata ticks collected in Croatia.
doi:10.1128/genomeA.01171-14
PMCID: PMC4223470  PMID: 25377719
7.  Draft Genome Sequence of Necropsobacter rosorum Strain P709T 
Genome Announcements  2014;2(5):e00913-14.
Necropsobacter is a recently described genus that contains a single species, N. rosorum, and belongs to the family Pasteurellaceae. Here, we present the draft genome of N. rosorum strain P709T, which is the first genome sequence from this species.
doi:10.1128/genomeA.00913-14
PMCID: PMC4192374  PMID: 25301642
8.  Draft Genome Sequence of Rickettsia aeschlimannii, Associated with Hyalomma marginatum Ticks 
Genome Announcements  2014;2(4):e00666-14.
Rickettsia aeschlimannii is a tick-associated human pathogen. We report here the draft genome of R. aeschlimannii strain MC16, isolated from Hyalomma marginatum marginatum ticks collected in Morocco.
doi:10.1128/genomeA.00666-14
PMCID: PMC4110219  PMID: 25059861
9.  Genome sequence and description of Bacteroides timonensis sp. nov. 
Standards in Genomic Sciences  2014;9(3):1181-1197.
Bacteroides timonensis strain AP1T (= CSUR P194 = DSM 26083) is the type strain of B. timonensis sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasoid female who suffered from severe anorexia nervosa. Bacteroides timonensis is a Gram-negative, obligate anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 7,130,768 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 43.3% and contains 5,786 protein-coding and 59 RNA genes, including 2 rRNA genes.
doi:10.4056/sigs.5389564
PMCID: PMC4148978  PMID: 25197491
Bacteroides timonensis; genome; culturomics; taxono-genomics
10.  Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov. 
Standards in Genomic Sciences  2014;9(3):1144-1158.
Collinsella massiliensis strain GD3T is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon.
doi:10.4056/sigs.5399696
PMCID: PMC4149003  PMID: 25197489
Collinsella massiliensis; genome; culturomics; taxono-genomics
11.  Genome sequence and description of Corynebacterium ihumii sp. nov. 
Standards in Genomic Sciences  2014;9(3):1128-1143.
Corynebacterium ihumii strain GD7T sp. nov. is proposed as the type strain of a new species, which belongs to the family Corynebacteriaceae of the class Actinobacteria. This strain was isolated from the fecal flora of a 62 year-old male patient, as a part of the culturomics study. Corynebacterium ihumii is a Gram positive, facultativly anaerobic, nonsporulating bacillus. Here, we describe the features of this organism, together with the high quality draft genome sequence, annotation and the comparison with other member of the genus Corynebacteria. C. ihumii genome is 2,232,265 bp long (one chromosome but no plasmid) containing 2,125 protein-coding and 53 RNA genes, including 4 rRNA genes. The whole-genome shotgun sequence of Corynebacterium ihumii strain GD7T sp. nov has been deposited in EMBL under accession number GCA_000403725.
doi:10.4056/sigs.5149006
PMCID: PMC4149009  PMID: 25197488
Corynebacterium ihumii; genome; culturomics; taxono-genomics
12.  Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov. 
Standards in Genomic Sciences  2014;9(3):970-986.
Enorma timonensis strain GD5T sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes.
doi:10.4056/sigs.4878632
PMCID: PMC4149031  PMID: 25197477
Enorma timonensis; genome; culturomics; taxono-genomics
13.  Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov. 
Standards in Genomic Sciences  2013;9(2):395-409.
Holdemania massiliensis strain AP2T sp. nov. is the type strain of H. massiliensis sp. nov., a new species within the genus Holdemania. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old French Caucasian female suffering from severe restrictive anorexia nervosa. H. massiliensis is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,795,625 bp-long genome (one chromosome but no plasmid) contains 3,461 protein-coding and 49 RNA genes, including 3 rRNA genes.
doi:10.4056/sigs.4628316
PMCID: PMC4062643  PMID: 24976895
Holdemania massiliensis; genome; culturomics; taxono-genomics
14.  Genome Sequence of Rickettsia gravesii, Isolated from Western Australian Ticks 
Genome Announcements  2013;1(6):e00975-13.
Rickettsia gravesii is a new Rickettsia species closely related to the human pathogen Rickettsia massiliae. Here, we describe the genome sequence of R. gravesii strain BWI-1, isolated from Amblyomma triguttatum triguttatum ticks collected from humans on Barrow Island, Western Australia.
doi:10.1128/genomeA.00975-13
PMCID: PMC3869331  PMID: 24285646
15.  Deciphering Genomic Virulence Traits of a Staphylococcus epidermidis Strain Causing Native-Valve Endocarditis 
Journal of Clinical Microbiology  2013;51(5):1617-1621.
We applied real-time genome sequencing to a Staphylococcus epidermidis strain that caused native-aortic-valve endocarditis in a 26-year-old patient. The 2.5-Mb genome from strain CSUR P278 exhibited a unique sequence type among S. epidermidis strains and contained 32 genes previously considered virulence genes in this species.
doi:10.1128/JCM.02820-12
PMCID: PMC3647915  PMID: 23363834
16.  Non-contiguous finished genome sequence and description of Nosocomiicoccus massiliensis sp. nov. 
Standards in Genomic Sciences  2013;9(1):205-219.
Nosocomiicoccus massiliensis strain NP2T sp. nov. is the type strain of a new species within the genus Nosocomiicoccus. This strain, whose genome is described here, was isolated from the fecal flora of an AIDS-infected patient living in Marseille, France. N. massiliensis is a Gram-positive aerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,645,244 bp long genome (one chromosome but no plasmid) contains 1,738 protein-coding and 45 RNA genes, including 3 rRNA genes.
doi:10.4056/sigs.4378121
PMCID: PMC3910558  PMID: 24501657
Nosocomiicoccus massiliensis; genome; culturomics; taxono-genomics
17.  Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov. 
Standards in Genomic Sciences  2013;8(3):525-538.
Megasphaera massiliensis strain NP3T sp. nov. is the type strain of Megasphaera massiliensis sp. nov., a new species within the genus Megasphaera. This strain, whose genome is described here, was isolated from the fecal flora of an HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,661,757 bp long genome (1 chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes, including 5 rRNA genes.
doi:10.4056/sigs.4077819
PMCID: PMC3910696  PMID: 24501636
Megasphaera massiliensis; genome; culturomics; taxonogenomics
18.  Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae 
Standards in Genomic Sciences  2013;8(2):336-351.
Dielma fastidiosa strain JC13T gen. nov., sp. nov. is the type strain of D. fastidiosa gen. nov., sp. nov., the type species of a new genus within the family Erysipelotrichaceae. This strain, whose draft genome is described here, was isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer. D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including 3 rRNA genes, whereas the plasmid contains 17 protein-coding genes.
doi:10.4056/sigs.3567059
PMCID: PMC3746426  PMID: 23991263
Dielma fastidiosa; Genome; Culturomics; Taxono-genomics
19.  Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae 
Standards in Genomic Sciences  2013;8(2):318-335.
Timonella senegalensis strain JC301T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels.
doi:10.4056/sigs.3476977
PMCID: PMC3746429  PMID: 23991262
Timonella senegalensis; genome; culturomics; taxono-genomics
20.  Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae 
Standards in Genomic Sciences  2013;8(2):290-305.
Enorma massiliensis strain phIT is the type strain of E. massiliensis gen. nov., sp. nov., the type species of a new genus within the family Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. E. massiliensis strain phIT is a Gram-positive, obligately anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,280,571 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901 protein-coding and 51 RNA genes, including 3 rRNA genes.
doi:10.4056/sigs.3426906
PMCID: PMC3746427  PMID: 23991260
Enorma massiliensis; genome; culturomics; taxono-genomics
21.  Non contiguous-finished genome sequence and description of Bacillus massiliosenegalensis sp. nov. 
Standards in Genomic Sciences  2013;8(2):264-278.
Bacillus massiliosenegalensis strain JC6T sp. nov. is the type strain of Bacillus massiliosenegalensis sp. nov., a new species within the genus Bacillus. This strain was isolated from the fecal flora of a healthy Senegalese patient. B. massiliosenegalensis is an aerobic Gram-positive rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,981,278-bp long genome comprises a 4,957,301-bp chromosome and a 23,977-bp plasmid. The chromosome contains 4,925 protein-coding and 72 RNA genes, including 4 rRNA genes. The plasmid contains 29 protein-coding genes.
doi:10.4056/sigs.3496989
PMCID: PMC3746431  PMID: 23991258
Bacillus massiliosenegalensis; genome; culturomics; taxono-genomics
22.  Genomic Analysis of Rickettsia japonica Strain YHT 
Journal of Bacteriology  2012;194(24):6992.
Rickettsia japonica strain YH, isolated in 1984 in Japan, is the type strain of R. japonica, the tick-borne agent of Japanese spotted fever. Here, we report the 1.33-Mb genome of this rickettsial species.
doi:10.1128/JB.01928-12
PMCID: PMC3510609  PMID: 23209240
23.  Genomic Comparison of Kingella kingae Strains 
Journal of Bacteriology  2012;194(21):5972.
Kingella kingae is a betaproteobacterium from the order Neisseriales, and it is an agent of invasive infections in children. We sequenced the genome from the septic arthritis strain 11220434. It is composed of a 1,990,794-bp chromosome but no plasmid, and it contains 2,042 protein-coding genes and 52 RNA genes, including 3 rRNA genes.
doi:10.1128/JB.01418-12
PMCID: PMC3486087  PMID: 23045489
24.  Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. 
Brevibacillus massiliensis strain phRT sp. nov. is the type strain of B. massiliensis sp. nov., a new species within the genus Brevibacillus. This strain was isolated from the fecal flora of a woman suffering from morbid obesity. B. massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%.
doi:10.4056/sigs.3466975
PMCID: PMC3739172  PMID: 23961307
Brevibacillus massiliensis; genome; culturomics; taxono-genomics
25.  Detection of Rickettsioses and Q fever in Sri Lanka 
Current serological evidence suggests the presence of scrub typhus and spotted fever group (SFG) rickettsiosis in Sri Lanka. Our objective was to identify rickettsial agents/Q fever as aetiological causes for patients who were presumed having rickettsioses by the presence of an eschar or a rash. Sera from patients with unknown origin fever from Matara were tested by immunofluorescence for SFG rickettsial antigens, typhus group rickettsiae, Orientia tsutsugamushi, and Coxiella burnetii antigens. Thirteen (7.3%) of the patients presented with a rash, 11 (6.1%) had an inoculation eschar, and 16 patients recalled a tick or flea bite. We found that 25 (14%) patients had scrub typhus, 6 (3%) SFG rickettsioses, 3 (1.6%) acute Q fever, 3 (1.6%) murine typhus, and 3 (1.6%) were infected by Rickettsia felis. In addition to already described scrub and murine typhus, we found that R. felis and C. burnetii infections should be considered in Sri Lanka.
doi:10.4269/ajtmh.2012.11-0424
PMCID: PMC3403782  PMID: 22492158

Results 1-25 (174)