Genome sequence and description of Coprococcus phoceensis gen. nov., sp. nov., a new bacterial genus isolated from the human left colon

We report here the main characteristics of Coprococcus phoceensis strain Marseille-P3062T (CSUR P3062). The 16S rDNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum analysis were used to identify and characterize this new anaerobic bacterial species, which was isolated from the left colon cleansing of a 25-year-old French man with Crohn's disease.

Genome sequence and description of Traorella massiliensis gen. nov., sp. nov., a new bacterial genus isolated from human left colon

A strictly anaerobic, motile, non-spore-forming, Gram-negative, rod-shaped bacterium designated Marseille-P3110T was isolated from the left colon cleansing of a 76-year-old Frenchwoman. Its 16S ribosomal RNA (rRNA) gene showed a 93.2% similarity level with the 16S rRNA of Dielma fastidiosa strain JC13, the closest species with a validly published name. The genome of Marseille-P3110T is 2 607 061 bp long with 35.99% G+C content. Of the 2642 predicted genes, 2582 were protein-coding genes and 60 were RNAs, including five 16S rRNA genes.

Corrigendum to "'Bacteroides mediterraneensis' sp. nov., a new human-associated bacterium isolated from ileum specimen"

[This corrects the article DOI: 10.1016/j.nmni.2016.06.003.].

Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics

Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.

Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics

The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

Chagas disease knocks on our door: a cross-sectional study among Latin American immigrants in Milan, Italy

OBJECTIVES

We aimed to assess the prevalence and risk factors for Chagas disease (CD) in Latin American immigrants and to evaluate the accuracy of diagnostic tests. Moreover, we offered to all positive subjects a complete free-of-charge clinical/instrumental evaluation as well as benznidazole treatment in order to stage the disease and verify drug tolerability.

METHODS

A cross-sectional survey of CD among Latin Americans living in Milan and its metropolitan area was conducted between July 2013 and July 2014. Blood samples were tested for serologic evidence of CD together with a questionnaire covering demographic and clinical-epidemiological information.

RESULTS

Forty-eight (9.6%) of the 501 tested subjects were conclusively diagnosed as having CD. The highest prevalence of CD was among those from Bolivia (43/169, 25.4%) and El Salvador (4/68, 5.9%). Older age (adjusted odds ratio (aOR)] 1.05, p =0.004), a Bolivian origin (aOR 8.80; p =0.003), being born in the department of Santa Cruz (aOR 3.72, p =0.047), having lived in mud houses (aOR 2.68; p =0.019), and having an affected relative (aOR 12.77, p =0.001) were independently associated with CD. The ARCHITECT Chagas test showed the highest sensitivity (100%) and specificity (99.8%). Twenty-nine of the subjects with CD (60.4%) underwent disease staging, 10 of whom (35.7%) showed cardiac and/or digestive involvement. Benznidazole treatment was associated with high frequency of adverse reactions (19/27, 70.4%) and permanent discontinuation (8/27, 29.6%).

CONCLUSIONS

CD is highly prevalent among Bolivians and Salvadorans living in Milan. Regions with a large Latin American immigrant population should implement programmes of active detection and treatment.

Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon

Strain Marseille-P2645T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non-spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed.

'Colibacter massiliensis' gen. nov., sp. nov., a new bacterial species isolated from human left colon

We present here the main characteristics of the strain Marseille-P2911 (= CSUR P2911 = DSMZ 103304), a bacterial species isolated from the left colon liquid sample of a 60-year-old man.

'Ileibacterium massiliense' gen. nov., sp. nov., a new bacterial species isolated from human ileum of a patient with Crohn disease

We propose here the main characteristics of 'Ileibacterium massiliense' strain Marseille-P3115, which was isolated from the ileum liquid sample of a patient with Crohn disease.

"Negativibacillus massiliensis" gen. nov., sp. nov., isolated from human left colon

We report here the main characteristics of "Negativibacillus massiliensis" strain Marseille-P3213T, isolated from a human left-colon wash sample.

'Colidextribacter massiliensis' gen. nov., sp. nov., isolated from human right colon

We report here the main characteristics of 'Colidextribacter massiliensis' strain Marseille-P3083T (CSURP3083), which was isolated from a human right colon lavage sample.

'Metaprevotella massiliensis' gen. nov., sp. nov., isolated from human ileum

We report here the main characteristics of 'Metaprevotella massiliensis' strain Marseille-P-3114T (CSURP3114) that was isolated from a human ileum sample.

'Caecibactermassiliensis' gen. nov., sp. nov., isolated from human right colon

We report here the main characteristics of 'Caecibacter massiliensis' strain Marseille-P-2974T (CSUR P2974), which was isolated from a human right colon sample.

'Traorella massiliensis' gen. nov., sp. nov., a new bacterial species isolated from the left colon of a 76-year-old woman

We present here the summary of main characteristics of 'Traorella massiliensis' strain Marseille-P3110T, which was isolated from a left colon liquid sample of a 76-year-old woman.

'Duodenibacillus massiliensis' gen. nov., sp. nov., a new species identified in human duodenum

We present here the main characteristics of 'Duodenibacillus massiliensis' strain Marseille-P2968, which was isolated from a human duodenum liquid sample of a 60-year-old man.

'Tidjanibacter massiliensis' gen. nov., sp. nov., a new bacterial species isolated from human colon

We report the summary of main characteristics of Tidjanibacter massiliensis strain Marseille-P3084T, a new bacterial species isolated from the liquid sample of the colon of a patient with a history of irritable bowel syndrome.

'Millionella massiliensis' gen. nov., sp. nov., a new bacterial species isolated from human right colon

We report here the main characteristics of 'Millionella massiliensis' strain Marseille-P3215^T (= CSUR P3215), which was isolated from a human right colon liquid sample.

'Angelakisella massiliensis' gen. nov., sp. nov., a new bacterial species isolated from human ileum

We present here a summary of the main characteristics of 'Angelakisella massiliensis' strain Marseille-P3217T (= CSUR P3217) that was isolated from the ileum liquid sample of a 76-year-old woman.

Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman

Massilioclostridium coli strain Marseille-P2976T (= CSUR P2976 = DSM 103344) is a new bacterial genus isolated from the left colon of a patient who underwent colonoscopy for colorectal cancer screening. Massilioclostridium coli is a Gram-negative bacillus, strict anaerobic, nonsporogenous and nonmotile organism. We describe here the strain Marseille-P2976T and provide its complete annotated genome sequence according to taxonogenomics concepts. Its genome is 2 985 330 bp long and contains 2562 predicted genes and 75 RNA genes.

Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach

Strain Marseille-P2915T, a Gram-positive, facultative anaerobic and nonmotile coccus, was isolated from the gastric lavage of a patient with severe anaemia. The 16S rRNA and rpoB gene comparison exhibited a sequence identity of 98.7 and 92.6% with Streptococcus infantis strain JCM 10157T, respectively, collocating it within the 'Streptococcus mitis' group. On the basis of phenotypic and genomic analysis, we propose the validation of the type strain Streptococcus timonensis sp. nov. Marseille-P2915T (= DSM 103349 = CSUR P2915).

'Merdibacter massiliensis' gen. nov., sp. nov., isolated from human ileum

We report here the main characteristics of 'Merdibacter massiliensis' strain Marseille-P3254T (= CSUR P3254 = DSM 103475), which was isolated from human ileum.

'Acidaminococcus timonensis' sp. nov. and 'Acidaminococcus massiliensis' sp. nov. isolated from human gut

We report here the main characteristics of 'Acidaminococcus timonensis' strain Marseille-P2764T, isolated from human right colon, and 'Acidaminococcus massiliensis' strain Marseille-P2828T, isolated from human duodenum.

'Intestinibacillus massiliensis' gen. nov., sp. nov., isolated from human left colon

We report here the main characteristics of ‘Intestinibacillus massiliensis’ strain Marseille-P3216^T that was isolated from a human left colon wash sample.

'Pseudoflavonifractor phocaeensis' gen. nov., sp. nov., isolated from human left colon

We describe here characteristics of ‘Pseudoflavonifractor phocaeensis’ strain Marseille-P3064^T, which was isolated from a human left colon wash sample.

Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum

The strain Marseille-P2749^T (= CSUR P2749 = DSM 103085) was isolated as part of culturomics study from a liquid duodenum sample from a French man. Bacterial cells were Gram-negative bacilli, fusiform shaped and non–spore forming, and they grew in microaerophilic and anaerobic atmosphere. Its genome is 1 809 169 bp long and contains 1646 protein-coding genes. The DNA G+C content was 27.33 mol%. This strain exhibited a 95.9% sequence similarity with Fusobacterium periodonticum, the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2749^T is suggested to be a novel species belonging to the genus Fusobacterium, for which the name Fusobacterium massiliense sp. nov. is proposed.

"Ihuprevotella massiliensis" gen. nov., sp. nov., isolated from human gut

We report here the main characteristics of "Ihuprevotella massiliensis" strain Marseille-P2826(T) (CSURP 2826) that was isolated from a human right colon lavage sample.

‘ Marseilla massiliensis ’ gen. nov., sp. nov., isolated from human right colon

We report here the main characteristics of ‘Marseilla massiliensis’ strain Marseille-P2475^T (CSURP2475) isolated from the human right colon.

'Mediterranea massiliensis' gen. nov., sp. nov., a new human-associated bacterium isolated from the right and left colon lavage of a 58-year-old patient

We report here the main characteristics of 'Mediterranea massiliensis' strain Marseille-P2645(T) (CSURP2645) that was isolated from stored samples of gut.

'Bacteroides mediterraneensis' sp. nov., a new human-associated bacterium isolated from ileum specimen

We report here the main characteristics of ‘Bacteroides mediterraneensis’ strain Marseille-P2644^T (CSURP2644) that was isolated from the stored samples of gut.

Romboutsia timonensis, a new species isolated from human gut

The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.