Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans.

BACKGROUND/OBJECTIVES: High salt intake has been linked to several diseases including obesity and an increased risk of death; however, fecal salinity and the ability of salt to alter the gut microbiota, which was recently identified as an instrumental factor for health and disease, remains poorly explored. METHODS/SUBJECTS: We analyzed the fecal samples of 1326 human individuals for salinity by refractometry, 572 for gut microbiota by culturomics, and 164 by 16S rRNA-targeted metagenomics. Geographical origin, age, gender, and obesity were tested as predictors of fecal salinity and halophilic diversity. All halophilic isolates were characterized by taxonogenomics and their genome sequenced. RESULTS: Fecal salinity was associated with obesity independently of geographical origin, gender, and age. The first 2 human-associated halophilic archaeal members were isolated along with 64 distinct halophilic species, including 21 new species and 41 known in the environment but not in humans. No halophiles grow in less than 1.5% salinity. Above this threshold, the richness of the halophilic microbiota was correlated with fecal salinity (r = 0.58, p < 0.0001). 16S metagenomics linked high fecal salinity to decreased diversity (linear regression, p < .035) and a depletion in anti-obesity Akkermansia muciniphila and Bifidobacterium, specifically B. longum and B. adolescentis. Genomics analysis suggested that halophilic microbes are not only transient passengers but may be residents of the human gut. CONCLUSIONS: High salt levels are associated with alteration of the gut microbial ecosystem and halophilic microbiota, as discovered during this study. Further studies should clarify if the gut microbiota alterations associated with high salt levels and the human halophilic microbiota could be causally related to human disease, such as obesity.

Corrigendum to 'Phoenicibacter congonensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman.

[This corrects the article DOI: 10.1016/j.nmni.2017.04.003.].

Study of Human Gastrointestinal Microbiota by Culturomics in Africa.

The interest in studying gut microbiota has been rekindled with the advent of molecular techniques, in particular, metagenomics. Culturomics (high throughput microbial culture with identification of the colonies by Maldi-TOF) has demonstrated its complementarity with metagenomics for comprehensive study of the microbiota. The main metagenomic studies have revealed an increase in biodiversity, with in particular an increase of Spirochaetes and Prevotella in subjects of African origin compared with Western subjects. Studies on malnutrition have shown a reduction of all bacteria and in particular of anaerobic bacteria and methanogenic archaea. Of the 1,162 bacteria isolated by culturomics studies, 476 were isolated only from non-African samples, 445 were isolated in African and non-African groups, and 241 bacteria were isolated from samples of African origin including 68 new species. Further studies of African microbiota by culturomics and metagenomics will make it possible to assess whether some bacteria have particular specificities and if these might play a role in certain pathologies such as malnutrition.

Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum.

Enterococcus timonensis sp. nov., strain Marseille-P2817T, is a facultatively anaerobic, motile and non-spore-forming Gram-positive coccus which was isolated from the sputum of a healthy adult man in Marseilles. We present herein its phenotypic description together with MALDI-TOF (matrix-assisted laser-desorption/ionization time-of-flight) mass spectrometry analysis and genome sequencing and comparison. The genome of Enterococcus timonensis is 2 123 933 bp long with 38.46 mol% of G+C content, and it contains 1983 protein-coding genes and 65 RNA genes (including nine rRNA genes).

'Brevibacterium ihuae' sp. nov., isolated from a stool sample of a healthy 25-year-old woman.

We report the main characteristics of 'Brevibacterium ihuae' strain cv3T isolated from a stool sample of a healthy 25-year-old woman.

'Bacteroides cutis,' a new bacterial species isolated from human skin.

We report the main characteristics of 'Bacteroides cutis' sp. nov., strain Marseille-P4118T (= CSUR P4118), a new species within the genus Bacteroides. This strain was isolated from a skin sample of a 75-year-old man from Marseille.

'Massilimalia timonensis' sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol.

We describe the main characteristics of a new bacterial species 'Massilimalia timonensis' sp. nov. The type strain Marseille-P3753T (=CSUR P3753) was isolated from the stool of a healthy Senegalese man.

'Lactobacillus raoultii' sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis.

We report the isolation of a new bacterium species, 'Lactobacillus raoultii' strain Marseille P4006 (CSUR P4006), isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis.

'Selenomonas massiliensis,' a new anaerobic bacterial species isolated from human oral microbiota.

We report the main characteristics of 'Selenomonas massiliensis' sp. nov., strain Marseille-P4036T (= CSUR P4036). The culturomic combined with taxonogenomic methods were used to identify and characterize this new anaerobic bacterial species, which was isolated from an oral sample of a 25-year-old healthy woman.

'Citricoccus massiliensis' sp. nov., a new bacterial species isolated from human skin by culturomics.

We report the main characteristics of 'Citricoccus massiliensis'strain Marseille-P4330, a new species within the genus Citricoccus. This strain was isolated from the skin of a healthy human man living in Dielmo, Senegal, Western Africa.

Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France.

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.

'Enterococcus timonensis' sp. nov., 'Actinomyces marseillensis' sp. nov., 'Leptotrichia massiliensis' sp. nov., 'Actinomyces pacaensis' sp. nov., 'Actinomyces oralis' sp. nov., 'Actinomyces culturomici' sp. nov. and 'Gemella massiliensis' sp. nov., new bacterial species isolated from the human respiratory microbiome.

We report the main characteristics of 'Enterococcus timonensis' strain Marseille-P2817T (CSUR P2817), 'Leptotrichia massiliensis' sp. nov., strain Marseille-P3007T (CSUR P3007), 'Actinomyces marseillensis' sp. nov., strain Marseille-P2818T (CSUR P2818), 'Actinomyces pacaensis' sp. nov., strain Marseille-P2985T (CSUR P2985), 'Actinomyces oralis' sp. nov., strain Marseille-P3109T (CSUR P3109), 'Actinomyces culturomici' sp. nov., strain Marseille-P3561T (CSUR P3561) and 'Gemella massiliensis' sp. nov., strain Marseille-P3249T (CSUR P3249) which were isolated from human sputum samples.

'Collinsella provencensis' sp. nov., 'Parabacteroides bouchesdurhonensis' sp. nov. and 'Sutterella seckii,' sp. nov., three new bacterial species identified from human gut microbiota.

We report here the main characteristics of 'Collinsella provencensis' strain Marseille-P3740 (CSUR P3740), 'Parabacteroides bouchesdurhonensis' strain Marseille-P3763 (CSUR P3763) and 'Sutterella seckii' strain Marseille-P3660 (CSUR P3660), which were isolated using culturomics from the human gut microbiota of healthy individuals living in Marseille.

Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool.

Strain Marseille-P3237 was isolated from a stool sample of a healthy 35-year-old Congolese pygmy female. This anaerobic, Gram-negative, non-spore-forming and non-motile coccus-shaped bacterium is a member of the order Coriobacteriales. It exhibits a 2 009 306-bp genome with a 65.46 mol% G+C content and is closely related to, but distinct from, members of the Olsenella genus. We propose the creation of the new genus Libanicoccus gen. nov. and of the new species Libanicoccus massiliensis sp. nov.

Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.

We present the description of Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.

Peptoniphilus lacydonensis sp. nov., a new human-associated species isolated from a patient with chronic refractory sinusitis.

Strain EL1T was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and genomic characteristics. This is a Gram stain-positive, anaerobic and microaerophilic coccus. Cells are catalase negative, nonmotile and non-spore forming. The major fatty acids are saturated hexadecanoic acid (34%), unsaturated 9-octadecenoic acid (32%) and 9.12-octadecadienoic acid (21%). The 1.86 Mb long genome exhibits a 29.9% G+C content and contains 1750 protein-coding and 43 RNA genes. On the basis of these data, we propose the creation of the new human-associated bacterial species Peptoniphilus lacydonensis sp. nov.

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.

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.

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.

Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'.

Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: 'Clostridium amazonitimonense' strain LF2T, 'Clostridium massilidielmoense' strain MT26T, 'Clostridium nigeriense' strain Marseille-P2414T and 'Clostridium merdae' strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.