The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev. 2015;28:237-264. [PMID: 25567229 DOI: 10.1128/cmr.00014-14]

Neoactinobaculum massilliense gen. nov., a new genesis and Pseudopropionibacterium massiliense sp. nov., a new bacterium isolated from the human oral microbiota

Neoactinobaculum massilliense gen. nov., strain Marseille-P6182^T (= CSUR P6182) and Pseudopropionibacterium massiliense sp. nov., strain Marseille-P6184^T (= CSUR P6184) are a new bacterial genus and new bacterial species belonging to the Actinobacteria phylum that have been isolated from the human oral microbiota.

Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection

Clostridium transplantifaecale strain Marseille-P8228T (= CSURP8228) is a new species isolated from a patient with recurrent Clostridium difficile infection.

Enterobacter timonensis sp. nov., a new bacterium isolated from a fresh human stool specimen

Enterobacter timonensis strain mt20T (= CSUR P2201T, = DSM101775T) is a new species isolated from a fresh human stool specimen.

Vaginisenegalia massiliensis gen. nov., sp. nov., a new bacterium isolated from the vagina flora and its taxono-genomic description

Strain Marseille-P5643T was isolated from a vaginal sample of a healthy Senegalese woman. It is an anaerobic Gram-negative, rod-shaped bacterium. Strain Marseille-P5643T exhibits 93.7% similarity levels with the Facklamia hominis strain ATCC 700628T, the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain Marseille-P5643T is 1.79 Mb with 39.0 mol% of G+C content. We propose here the creation of Vaginisenegalia massiliensis gen. nov., sp. nov., as a new bacterial genus from the phylum Firmicutes.

Corynebacterium pacaense sp. nov., Alistipes megaguti sp. nov., Alistipes provencensis sp. nov., 3 new bacteria isolated from fresh human stool specimens

Here we describe the basic characteristics of Corynebacterium pacaense strain Marseille-P2417T (= CSUR P2417), Alistipes megaguti strain Marseille-P5997T (= CSUR P5997) and Alistipes provencensis strain Marseille-P2431T (= CSUR P2431 = DSM 102308). The phenotypic criteria, the 16S ribosomal RNA sequencing and MALDI-TOF MS spectra analysis were used to identify and characterize these new bacteria species, which were isolated from fresh human stool specimens.

Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen

Parabacteroides massiliensis sp. nov., strain Marseille-P2231T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It was isolated from a stool specimen of a 25-year-old healthy woman. Its genome was 5 013 798 bp long with a 45.7 mol% G+C content. The closest species based on 16S rRNA sequence was Parabacteroides merdae strain JCM 9497T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides.

Akkermansia muciniphila is a promising probiotic

Akkermansia muciniphila (A. muciniphila), an intestinal symbiont colonizing in the mucosal layer, is considered to be a promising candidate as probiotics. A. muciniphila is known to have an important value in improving the host metabolic functions and immune responses. Moreover, A. muciniphila may have a value in modifying cancer treatment. However, most of the current researches focus on the correlation between A. muciniphila and diseases, and little is known about the causal relationship between them. Few intervention studies on A. muciniphila are limited to animal experiments, and limited studies have explored its safety and efficacy in humans. Therefore, a critical analysis of the current knowledge in A. muciniphila will play an important foundation for it to be defined as a new beneficial microbe. This article will review the bacteriological characteristics and safety of A. muciniphila, as well as its causal relationship with metabolic disorders, immune diseases and cancer therapy.

Massilicoli timonensis sp. nov., a new bacterium isolated from the human microbiota

Massilicoli timonensis sp. nov., strain Marseille-P3755T (= CSUR P3755 = DSM 103513) is a new bacterial species from the phylum Firmicutes and the family Clostridiales which was isolated from the human gut microbiota.

Enterococcus mediterraneensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy

Enterococcus mediterraneensis strain Marseille-P4358T (= CSURP4358T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo.

Olsenella timonensis sp. nov., a new bacteria species isolated from the human gut microbiota

Olsenella timonensis sp. nov., strain Marseille-P2300T (= CSUR P2300; =DSM102072), is a new bacterial species from the phylum Firmicutes in the family Atopobiaceae.This bacteria species was isolated from the human gut microbiota.

Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care

Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine.

Dorea phocaeensis sp. nov., a new bacterium isolated from the stool of a healthy 29-year-old male

Dorea phocaeensis strain Marseille-P4003^T (= CSURP4003^T; = CCUG71359^T) is a new species isolated from the stool of a healthy 29-year-old male from France.

Whole-Genome Sequence of Haloimpatiens lingqiaonensis Strain P8956

In 2016, Haloimpatiens lingqiaonensis was described as a bacterial isolate from paper mill wastewater. Previously, no whole-genome sequence was available for this microorganism. Whole-genome sequencing of strain P8956 yielded a 3,295,388-bp genome with a 30.7% G+C content, 2,917 protein-coding genes, and 95 predicted RNA genes.

In 2016, Haloimpatiens lingqiaonensis was described as a bacterial isolate from paper mill wastewater. Previously, no whole-genome sequence was available for this microorganism. Whole-genome sequencing of strain P8956 yielded a 3,295,388-bp genome with a 30.7% G+C content, 2,917 protein-coding genes, and 95 predicted RNA genes.

Extensive culturomics of 8 healthy samples enhances metagenomics efficiency

Molecular approaches have long led to the assumption that the human gut microbiota is dominated by uncultivable bacteria. The recent advent of large-scale culturing methods, and in particular that of culturomics have demonstrated that these prokaryotes can in fact be cultured. This is increasing in a dramatic manner the repertoire of commensal microbes inhabiting the human gut. Following eight years of culturomics approach applied on more than 900 samples, we propose herein a remake of the pioneering study applying a dual approach including culturomics and metagenomics on a cohort of 8 healthy specimen. Here we show that culturomics enable a 20% higher richness when compared to molecular approaches by culturing 1 archaeal species and 494 bacterial species of which 19 were new taxa. Species discovered as a part of previous culturomics studies represent 30% of the cultivated isolates, while sequences derived from these new taxa enabled to increase by 22% the bacterial richness retrieved by metagenomics. Overall, 67% of the total reads generated were covered by cultured isolates, significantly reducing the hidden content of sequencing methods compared to the pioneering study. By redefining culture conditions to recover microbes previously considered fastidious, there are greater opportunities than ever to eradicate metagenomics dark matter.

Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections

Background

Irritable bowel syndrome (IBS) is a chronic and debilitating functional gastrointestinal disorder affecting 9%-23% of the population across the world. The relative efficacy of fecal microbiota transplantation (FMT) on IBS symptoms was demonstrated in a double-blind, randomized study.

Methods

We describe the case of a 73-year-old woman suffering from IBS (abdominal pain, bloating, and abundant and disabling diarrhea, with 10-15 stools a day) and repetitive urinary tract infection (UTI; 5 episodes in 6 months, including 3 the last 2 months) for several years, generating an impaired quality of life. She received an FMT with 400 mL of fecal infusion from a healthy donor via a nasogastric tube after bowel lavage. Her digestive microbiota was analyzed using culturomic and metagenomic targeting 16S rRNA sequencing methods.

Results

Eight months after transplantation, we observed a significant reduction in frequency and improvement in stool consistency (3-4 molded stools a day against 10-15 before the transplant) and no recurrence of urinary infection (as previously reported). Using culturomics, we found 12 bacteria present in the fecal infusion and post-transplant stool; these were absent pretransplant. Three of them (Intestinimonas massiliensis, Oscillibacter massiliensis, and Provencibacter massiliensis) were previously discovered and cultivated in our laboratory using culturomics. Using metagenomics, we also observed 12 bacteria, different from those observed during culture, that could have been transferred to the patient by FMT.

Conclusions

In this case report, IBS symptoms and UTI frequency decreased after FMT UTI. Further studies involving more patients would be relevant to confirm this work and develop bacteriotherapy.

Colonization of Cutibacterium avidum during infant gut microbiota establishment

Establishment of the infant gut microbiota affects gut maturation and influences long-term health. Cutibacterium (formerly Propionibacterium) have been identified as early colonizers, but little is known about their function. Using a cultivation-dependent and -independent approach, we determined Cutibacterium prevalence, diversity and functional potential. In feces from a Swiss infant cohort (n = 38), prevalence of Propionibacterium/Cutibacterium decreased from 84% at 2 weeks, to 65% at 4 weeks, 47% at 8 weeks and 41% at 12 weeks of age. Abundance varied among individuals, and persistence depended on the colonization levels at 2 weeks. Cutibacterium isolates (n = 87) were obtained from 10 infants from a smaller cohort (n = 12); restriction fragment length polymorphism clustered isolates in four groups, and all identified as Cutibacterium avidum. Colonization potential and metabolic effects of C. avidum addition were tested in an in vitro continuous intestinal fermentation model mimicking infant proximal colon conditions. Cutibacterium avidum spiked daily at 108 or 109 cells mL-1 colonized, decreased formate and persisted during the washout period. Significant correlations were observed between Propionibacterium/Cutibacterium and lactate-producers and protein-degraders in both reactors and infant feces. Our findings highlight the natural presence of C. avidum and its role as a lactate-consumer and propionate-producer in infants younger than 3 months.

Genome Sequence of Enorma sp. Strain Marseille-P9525 T , a Member of a Human Gut Microbiome

Strain Marseille-P9525^T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb (G+C content, 66.8%) draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525^T represents a new species to be described.

Strain Marseille-P9525^T was isolated from the gut microbiota of a 28-year-old woman and exhibits a 2.23-Mb (G+C content, 66.8%) draft genome sequence containing 1,902 protein-coding genes, 49 tRNAs, and 3 rRNAs. The 16S rRNA sequencing and in silico DNA-DNA hybridization indicated that strain Marseille-P9525^T represents a new species to be described.

Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection

Prevotella marseillensis strain Marseille-P8229^T (= CSURP8229) is a new species isolated from a patient with recurrent Clostridium difficile infection. It is an anaerobic, non-motile, non-spore-forming Gram-negative coccobacillus isolated from the stool of patient with recurrent Clostridium difficile infection in Marseille. We present herein its phenotypic description together with MALDI-TOF mass spectrometry analysis and genome sequencing and comparison. The genome of P. marseillensis is 4.1607 Mbp long with 45.80 mol% of G+C content, and it contains 3078 protein-coding genes.

Prevotella ihumii sp. nov., a new bacterium isolated from a stool specimen of a healthy woman

Prevotella ihumii strain Marseille-P3385^T (= CSURP3385^T; = DSM106428^T) is a new species isolated from a fresh stool specimen of a healthy woman.

A Literature Review of Metagenomics and Culturomics of the Peri-implant Microbiome: Current Evidence and Future Perspectives

Background and objectives: In recent years, many different culture-independent molecular techniques have been developed with the aim of investigating the not yet cultivated part of the resident flora of the oral cavity and of analyzing the peri-implant and periodontal flora both in healthy and diseased sites. The most used technologies are Roche 454 pyrosequencing, Illumina HiSeq/MiSeq, ABI SOLiD and Ion Torrent. Due to these methods, two different approaches are available: Metagenomics and the 16S gene analysis. A complementary strategy was also recently developed: Culturomics. Culturomics consists of different culture conditions that allow a very rapid bacterial identification. The focused question of this review was developed in PICO format in order to investigate the role of metagenomics, 16S gene analysis and culturomics (interventions) in the differential study (comparison) of the peri-implant and periodontal microbiome (outcome) in humans (participants). The secondary aim was the characterization of currents limits and future applications of the three techniques. Methods: The authors performed a literature search on three databases (Web of Science, Scopus and PubMed) from 01/01/2003 to 31/06/2019. Date of last search was: 25/08/19. Any type of article dealing with the analysis of periodontal and peri-implant flora with metagenomic, culturomic or 16S gene analysis was included. No language restrictions were applied. Risk of bias for RCT was assessed using the Cochrane collaboration's tool whereas case-control and cohort studies were evaluated through the Newcastle-Ottawa scale. Results: The initial search resulted in 330 titles in total. After careful evaluation of all results no studies were found to satisfy the primary outcome of the present review. Hence a narrative review dealing with the secondary aim was performed. Conclusions: Metagenomic and 16S gene analysis approaches contributed in clarifying some crucial aspects of the oral microbiome. Based on the reported evidence some bacteria could be found around teeth and implants even in the absence of signs of inflammation and other species are more frequently found in supragingival peri-implant biofilm. Teeth and implants (even if adjacent) seem not to share the same microbiome and healthy teeth have a more diversified one. The same analyses also highlighted that the oral biofilm of smokers is composed by more periodontopathogen bacteria compared to non-smokers and that geographical location and ethnicity seem to play a role in bacterial composition. Culturomics, which has not yet been applied to the study of oral microbiota, consists of the use of different culture conditions and of the identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with the aim of increasing the bacterial repertoire and avoiding the limits of molecular methods. In order to better evaluate perspectives and limits of the all presented approaches further studies comparing the different molecular techniques are encouraged. This review received no funding.

Identification performance of MALDI-ToF-MS upon mono- and bi-microbial cultures is cell number and culture proportion dependent

Biotyping using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) mass spectroscopy (MS) has revolutionized microbiology by allowing clinicians and scientists to rapidly identify microbes at genus and species levels. The present study extensively assesses the suitability and reliability of MALDI-ToF biotyping of 14 different aerobic and anaerobic bacterial species as pure and mixed cultures. Reliable identification at species level was possible from biomaterial of older colonies and even frozen biomaterial, although this was species dependent. Using standard instrument settings and direct application of biomaterial onto the MALDI-ToF target plates, it was determined that the cell densities necessary for completely reliable identification of pure cultures varied between 2.40 × 10⁸ and 1.10 × 10¹⁰ viable cell counts (VCCs) per mL, depending on the species. Evaluation of the mixed culture algorithm of the Bruker Biotyper^® software showed that the performance of the algorithm depends greatly on the targeted species, on their phylogenetic distance, and on their ratio of VCC per mL in the mixed culture. Hence, the use of MALDI-ToF-MS with incorporation of the mixed culture algorithm of the software is a useful pre-screening tool for early identification of contaminants, but due to the great variability in performance between different species and the usually unknown percentage of the possible contaminant in the mixture, it is advisable to combine this method with other microbiology methods.

Metagenomic and culturomic analysis of gut microbiota dysbiosis during Clostridium difficile infection

Recently, cocktail of bacteria were proposed in order to treat Clostridium difficile infection (CDI), but these bacteriotherapies were selected more by chance than experimentation. We propose to comprehensively explore the gut microbiota of patients with CDI compared to healthy donors in order to propose a consortium of bacteria for treating C. difficile. We compared stool samples composition from 11 CDI patients and 8 healthy donors using two techniques: metagenomics, 16S V3-V4 region amplification and sequencing and culturomics, high throughout culture using six culture conditions and MALDI-TOF identification. By culturomics, we detected 170 different species in the CDI group and 275 in the control group. Bacteroidetes were significantly underrepresented in the CDI group (p = 0.007). By metagenomics, 452 different operational taxonomic units assigned to the species level were detected in the CDI group compared to 522 in the control group. By these two techniques, we selected 37 bacteria only found in control group in more than 75% of the samples and/or with high relative abundance, 10 of which have already been tested in published bacteriotherapies against CDI, and 3 of which (Bifidobacterium adolescentis, Bifidobacterium longum and Bacteroides ovatus) have been detected by these two techniques. This controlled number of bacteria could be administrated orally in a non-invasive way in order to treat CDI.

Varibaculum massiliense sp. nov., a new bacterium isolated from human urine with culturomics

Varibaculum massiliense sp. nov. strain Marseille-P2802^T (= CSUR P2802 = DSM 103074) is a new species within the genus Varibaculum in the phylum Actinobacteria that was isolated from the urine of a 59-year-old man treated with chronic haemodialysis for diabetic nephropathy.

Corynebacterium senegalense sp. nov. and Arthrobacter senegalensis sp. nov., two new Actinobacteria isolated from skin swab from the palm of hand

Corynebacterium senegalense strain Marseille-P4329^T (= CSURP4329) and Arthrobacter senegalensis strain Marseille-P4329^T (= CSURP4198) are new species first isolated from human skin. A culturomics approach and taxonogenomics methods were used for these new bacterial species.

Selenomonas felix sp. nov., a new bacterium isolated from human sputum

Selenomonas felix strain Marseille-P3560T (=CSURP3560) is a new species isolated from human sputum.

Massilimicrobiota timonensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota

Massilimicrobiota timonensis gen. nov., sp. nov. strain Marseille-P2264 is a new species from Firmicutes phylum isolated from the human gut. Its genome was 2,849,574 bp-long with a 31.8% G+C content. The closest species based on 16S rRNA sequence was Longibaculum muris with 95.6% sequence similarity. Considering phenotypic features, 16S rRNA sequence and comparative genome studies, we proposed Marseille-P2264 as the type strain of Massilimicrobiota timonensis gen. nov., sp. nov.

Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child

Based on our phenotypic and genotypic analyses, Brachybacterium massiliense strain Marseille-P2240T (= CSURP2240; = DSM 101766) is a new species isolated from stool of a healthy subject. The strain was stained Gram-positive. It was aerobic, catalase-positive and oxidase-negative. Its optimal growth occurs at 37°C in aerobic condition. The 16S ribosomal RNA sequence analysis revealed that strain Marseille-P2240T shown 98.18% similarity with Brachybacterium saurashtrense strain JG 06, the more closely related species with standing in nomenclature.

Corynebacterium bouchesdurhonense sp. nov., and Corynebacterium provencense sp. nov., two new species isolated from obese patients

Corynebacterium bouchesdurhonense sp. nov. strain Marseille-P2067T (= CSURP2067; = DSM100846) and Corynebacterium provencense sp. nov. strain Marseille-P2161T (= CSURP2161; = DSM101074) are two new species from the order Corynebacteriales that were isolated from obese French individuals.

Varibaculum timonense sp. nov., a new bacterial species isolated from human stool sample

Varibaculum timonense sp. nov. strain Marseille-P3369T (= CSURP3369) is a new species from the order Actinomycetales that has been isolated from a fresh stool sample of a healthy French woman.

Acidaminococcus provencensis sp. nov., a new bacterium isolated from a fresh human stool specimen

Acidaminococcus provencensis strain Marseille-P4266T (= CSURP4266T) is a new species isolated from a fresh human stool specimen.

Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women

Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: Arcanobacterium ihumii sp. nov. strain Marseille-P5647T, Varibaculum vaginae sp. nov. strain Marseille-P5644T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995T, which we describe according to the concept of taxonogenomics.

Brachybacterium timonense sp. nov., a new bacterium isolated from human sputum

Brachybacterium timonense strain Marseille-P4339T (=CSURP4339, =CECT9821) is a new species isolated from human sputum.

Corynebacterium urinapleomorphum sp. nov., a new bacterial species isolated from human urine sample

Corynebacterium urinapleomorphum sp. nov. stain Marseille-P2799T (= CSURP2799; = DSM103272) is a new species from the order Corynebacteriales that was isolated from urine of a 2-month-old child with gastroenteritis.

Genome sequence and description of Bacteroides bouchesdurhonensis sp. nov., a new anaerobic bacterium isolated from the human gut

Bacteroides bouchesdurhonensis sp. nov., strain Marseille-P2653T (= CSUR; P2653=DSM103120) is a new bacterial species belonging to the Firmicutes phylum in the family Bacteroidaceae that was isolated from the human gut microbiota.

Gut microbiome: An intermediary to neurotoxicity

There is growing recognition that the gut microbiome is an important regulator for neurological functions. This review provides a summary on the role of gut microbiota in various neurological disorders including neurotoxicity induced by environmental stressors such as drugs, environmental contaminants, and dietary factors. We propose that the gut microbiome remotely senses and regulates CNS signaling through the following mechanisms: 1) intestinal bacteria-mediated biotransformation of neurotoxicants that alters the neuro-reactivity of the parent compounds; 2) altered production of neuro-reactive microbial metabolites following exposure to certain environmental stressors; 3) bi-directional communication within the gut-brain axis to alter the intestinal barrier integrity; and 4) regulation of mucosal immune function. Distinct microbial metabolites may enter systemic circulation and epigenetically reprogram the expression of host genes in the CNS, regulating neuroinflammation, cell survival, or cell death. We will also review the current tools for the study of the gut-brain axis and provide some suggestions to move this field forward in the future.

Whole-Genome Sequence of French Clinical Olivibacter jilunii Strain P8502

In 2013, Olivibacter jilunii was reported as a bacterial species isolated from contaminated soil. In 2018, a clinical strain from the same species was isolated from the rectal swab of a Hajj pilgrim. Genome sequencing yielded 6,704,032 bp, with 41.2% G+C content, 5,406 protein-coding genes, and 54 predicted RNA genes in strain P8502.

In 2013, Olivibacter jilunii was reported as a bacterial species isolated from contaminated soil. In 2018, a clinical strain from the same species was isolated from the rectal swab of a Hajj pilgrim. Genome sequencing yielded 6,704,032 bp, with 41.2% G+C content, 5,406 protein-coding genes, and 54 predicted RNA genes in strain P8502.

Lysinibacillus timonensis sp. nov., Microbacterium timonense sp. nov., and Erwinia mediterraneensis sp. nov., three new species isolated from the human skin

Lysinibacillus timonensis strain Marseille-P5727^T (=CSURP5727), Microbacterium timonense strain Marseille-P5731^T (=CSURP5731) and Erwinia mediterraneensis strain Marseille-P5165^T (=CSURP5165) are three new species isolated from the human skin.

Modelling approaches for studying the microbiome

Advances in metagenome sequencing of the human microbiome have provided a plethora of new insights and revealed a close association of this complex ecosystem with a range of human diseases. However, there is little knowledge about how the different members of the microbial community interact with each other and with the host, and we lack basic mechanistic understanding of these interactions related to health and disease. Mathematical modelling has been demonstrated to be highly advantageous for gaining insights into the dynamics and interactions of complex systems and in recent years, several modelling approaches have been proposed to enhance our understanding of the microbiome. Here, we review the latest developments and current approaches, and highlight how different modelling strategies have been applied to unravel the highly dynamic nature of the human microbiome. Furthermore, we discuss present limitations of different modelling strategies and provide a perspective of how modelling can advance understanding and offer new treatment routes to impact human health.

Bifidobacterium and Lactobacillus Composition at Species Level and Gut Microbiota Diversity in Infants before 6 Weeks

Our objective was to investigate the effects of different delivery and feeding modes on the gut microbiota composition of early infants with special emphasis on Bifidobacterium and Lactobacillus profiles at species level. 16S rRNA V3-V4 regions, bifidobacterial, and lactobacilli groEL genes from infant feces were sequenced by Illumina MiSeq. Gut microbiota abundance was significantly different, where standard vaginally delivered (SVD) and breast-fed (BF) groups were higher in comparison with caesarean section (CS), milk-powder-fed (MPF), and mixed-fed (MF) groups. The genus unclassified Enterobacteriaceae was dominant, followed by Bifidobacterium, which was highly abundant in SVD and BF groups. The dominant Bifidobacterium species in all groups were B. longum subsp. longum, B. longum subsp. infantis and B. animalis subsp. lactis. B. dentium and the diversity of Bifidobacterium in SVD and BF groups were significantly higher. For Lactobacillus profiles, L. rhamnosus and L. gasseri were dominant among all the groups, while Lactobacillus species in CS and MPF groups were more diverse. Functional predictions showed significant differences between delivery mode and feeding groups, such as phosphotransferase system as well as taurine and hypotaurine metabolism. In early infants with different delivery and feeding methods, gut microbiota-particularly bifidobacteria and lactobacilli communities-showed significant differences, with strong implications for physiological functions.

Variation of cultured skin microbiota in mothers and their infants during the first year postpartum

BACKGROUND/OBJECTIVES

The establishment of newborn skin flora depends on the ongoing skin maturation and the existence of potential microbial colonizers within the environment of the infant during a period of intense mother-infant physical interaction. This longitudinal study assessed culturable skin bacteria in the mother-infant dyad during the first year of life.

METHODS

A total of 17 mother-infant dyads were swabbed within 24 hours postpartum and at 3, 6, 9, and 12 months. Skin swabbing was performed on two anatomical areas per individual (mothers: chest-abdomen; infants: forehead-buttocks) and were incubated in five different solid culture media to optimize yield. Isolated bacterial species were identified to genus or species level using the API system (BioMeriéux, Marcy l'Etoile, France).

RESULTS

A total of 444 microbial strains were isolated belonging to 22 genera: 6 "frequent" (isolated from > 5% samples: S aureus, Proteus, Klebsiella, Pseudomonas, Enterobacter, and Enterococcus) and 16 "infrequent." Isolated genera per individual peaked at 6 months postpartum for mothers and infants (P < 0.05). Enterobacter, Enterococcus, Klebsiella, and Pseudomonas isolation rates varied significantly as a function of sampling time contrary to the rather constant isolation rates of Proteus and S aureus. The rates of concordant isolation of the same microbial species within the mother-infant dyad tended to drop from birth to the end of the first year postpartum.

CONCLUSIONS

Distinct variations in the isolation rates of skin commensals from specific anatomical sites of the mother-infant dyad indicate bidirectional microbial transmission. Increasing skin flora individuality of the growing infant was recorded, manifested by declining rates of concordant isolation of the same microbial species from mother and her infant.

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.

Virgibacillus ndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy

Virgibacillus ndiopensis strain Marseille-P3835T (= CSURP3835T; = CCUG70388T) is a new specie isolated from the stool of a healthy 11-year-old boy from N'Diop, Senegal.

Evaluation of gut bacterial community composition and antimicrobial resistome in pregnant and non-pregnant women from Saudi population

Background: Gut microbiota (GM) has recently been described as a functional reservoir of antimicrobial resistant genes (ARGs). However, the ARG-carrying bacterial species in the human gut has been poorly studied. This study, for the first time, is reporting bacterial communities' composition and antimicrobial resistome in the stool samples of pregnant and non-pregnant (NP) Saudi females. Methods: Gut bacterial community composition was analyzed by 16S amplicon sequencing and culturomics. High throughput MALDI-TOF technique was used for identification of the isolates from stool samples and evaluated for resistance against 13 antibiotics using the agar dilution method. Clinically important ARGs were PCR amplified from genomic DNA of the stool samples using gene-specific primers. Results: 16S amplicon sequencing revealed that GM of pregnant and NP women were predominantly comprised of phyla Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Bacterial diversity decreased in pregnant groups, whereas phylum Bacteroidetes declined significantly (p<0.05) in the first trimester. We noticed a relatively high abundance of butyrate-producing bacteria (eg, Faecalibacterium spp. and Eubacterium spp.) in the gut of pregnant women, whereas Prevotella copri was found at significantly (p<0.01) higher abundance in NP women. Moreover, about 14,694 isolates were identified and classified into 132 distinct species. The majority of the species belonged to phyla Firmicutes and Proteobacteria. About 8,125 isolates exhibited resistance against antibiotics. Out of 73 resistant-species, Enterococcus was the most diverse genus and Escherichia coli was the highly prevalent bacterium. The majority of the isolates were resistant to antibiotics; trimethoprim/sulfamethoxazole, cycloserine, and cefixime. ARGs encoding resistance against aminoglycoside, macrolide, quinolone, β-lactam, and tetracycline antibiotics were predominantly found in genomic DNA of the stool samples. Conclusion: We conclude that pregnancy-associated GM modulations may help to sustain a healthy pregnancy, but a higher proportion of antibiotic resistance could be deleterious for both maternal and fetal health.

The Lung Microbiome and Its Role in Pneumonia

The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.

The Microbiome and Irritable Bowel Syndrome - A Review on the Pathophysiology, Current Research and Future Therapy

Irritable bowel syndrome (IBS) is a functional disorder which affects a large proportion of the population globally. The precise etiology of IBS is still unknown, although consensus understanding proposes IBS to be of multifactorial origin with yet undefined subtypes. Genetic and epigenetic factors, stress-related nervous and endocrine systems, immune dysregulation and the brain-gut axis seem to be contributing factors that predispose individuals to IBS. In addition to food hypersensitivity, toxins and adverse life events, chronic infections and dysbiotic gut microbiota have been suggested to trigger IBS symptoms in tandem with the predisposing factors. This review will summarize the pathophysiology of IBS and the role of gut microbiota in relation to IBS. Current methodologies for microbiome studies in IBS such as genome sequencing, metagenomics, culturomics and animal models will be discussed. The myriad of therapy options such as immunoglobulins (immune-based therapy), probiotics and prebiotics, dietary modifications including FODMAP restriction diet and gluten-free diet, as well as fecal transplantation will be reviewed. Finally this review will highlight future directions in IBS therapy research, including identification of new molecular targets, application of 3-D gut model, gut-on-a-chip and personalized therapy.

Filling the gap between collection, transport and storage of the human gut microbiota

Stool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity.

Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut

As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.

Actinobacteria and Cyanobacteria Diversity in Terrestrial Antarctic Microenvironments Evaluated by Culture-Dependent and Independent Methods

Bacterial diversity from McMurdo Dry Valleys in Antarctica, the coldest desert on earth, has become more easily assessed with the development of High Throughput Sequencing (HTS) techniques. However, some of the diversity remains inaccessible by the power of sequencing. In this study, we combine cultivation and HTS techniques to survey actinobacteria and cyanobacteria diversity along different soil and endolithic micro-environments of Victoria Valley in McMurdo Dry Valleys. Our results demonstrate that the Dry Valleys actinobacteria and cyanobacteria distribution is driven by environmental forces, in particular the effect of water availability and endolithic environments clearly conditioned the distribution of those communities. Data derived from HTS show that the percentage of cyanobacteria decreases from about 20% in the sample closest to the water source to negligible values on the last three samples of the transect with less water availability. Inversely, actinobacteria relative abundance increases from about 20% in wet soils to over 50% in the driest samples. Over 30% of the total HTS data set was composed of actinobacterial strains, mainly distributed by 5 families: Sporichthyaceae, Euzebyaceae, Patulibacteraceae, Nocardioidaceae, and Rubrobacteraceae. However, the 11 actinobacterial strains isolated in this study, belonged to Micrococcaceae and Dermacoccaceae families that were underrepresented in the HTS data set. A total of 10 cyanobacterial strains from the order Synechococcales were also isolated, distributed by 4 different genera (Nodosilinea, Leptolyngbya, Pectolyngbya, and Acaryochloris-like). In agreement with the cultivation results, Leptolyngbya was identified as dominant genus in the HTS data set. Acaryochloris-like cyanobacteria were found exclusively in the endolithic sample and represented 44% of the total 16S rRNA sequences, although despite our efforts we were not able to properly isolate any strain from this Acaryochloris-related group. The importance of combining cultivation and sequencing techniques is highlighted, as we have shown that culture-dependent methods employed in this study were able to retrieve actinobacteria and cyanobacteria taxa that were not detected in HTS data set, suggesting that the combination of both strategies can be usefull to recover both abundant and rare members of the communities.