Search

The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) ( n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate., Competing Interests: The authors declare no conflicts of interest.

Introduction: Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date., Methods: In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics., Results: Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples., Conclusion: This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting., Competing Interests: DR was a consultant in microbiology for the Hitachi High-Tech Corporation until March 2021. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be misconstrued as a potential conflict of interest., (Copyright © 2023 Naud, Valles, Abdillah, Abou Chacra, Mekhalif, Ibrahim, Caputo, Baudoin, Gouriet, Bittar, Lagier, Ranque, Fenollar, Tidjani Alou and Raoult.)

Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.

Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm 3 and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.

Background: Currently, Candida auris is among the most serious emerging pathogens that can be associated with nosocomial infections and outbreaks in intensive care units. Clinicians must be able to identify and manage it quickly., Objective: Here, we report for the first time in Algeria seven cases of C. auris infection or colonisation., Methods and Results: The strains were isolated from clinical sites including bronchial aspirates (n = 4), wound swabs (n = 1), urine sample (n = 1) and peritoneal fluid (n = 1), in patients admitted to the intensive care unit. Candida auris was identified both by MALDI-TOF and by sequencing the ITS region and the D1/D2 domain. Antifungal susceptibility testing was performed using the E-test method. Non-wildtype susceptibility was observed for five strains against fluconazole, itraconazole, voriconazole and caspofungin. Genotyping showed the presence of four clades (I-IV) in one hospital., Conclusions: Appropriate antifungal treatments with rapid and accurate microbial identification are the cornerstone for the management and control of C. auris infections., (© 2022 The Authors. Mycoses published by Wiley-VCH GmbH.)

The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.

Microorganisms not yet cultured represent a large proportion of the microbes described to date. Progress in sequencing and metagenomic tools continues to increase microbial diversity without providing information on their physiological and pathophysiological characteristics, such as the recent discovery of enigmatic microbes belonging to Candidate Phyla Radiation (CPR). Reverse genomics is a recent technique allowing co-cultivation of a few CPR members, affiliated to the Saccharibacteria phylum, based on the analysis of their already-available genomes. Here, our aim is to designate a common system capable of cultivating any given taxon of this phylum from human samples. We managed to design, in silico, 11 common epitopes for all Saccharibacteria species recovered from the human oral cavity and which can serve as antigens via bioinformatics analyses. These sequences allow the synthesis of target antibodies, sorting Saccharibacteria spp. by flow cytometry and co-culturing them afterwards with adapted hosts. This epitope set can facilitate the cultivation of CPR in general, which in recent years has been considered a challenge for microbiologists, and subsequently contributes to better studying this new branch on the tree of life.

The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR ( Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, " Candidatus Minimicrobia naudis" and " Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the C T values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.

Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new branch, thanks to the intensive application of metagenomics and sequencing technologies. CPR have been eventually identified by 16S rRNA analysis, and they represent more than 26% of microbial diversity. Despite their ultrasmall size, reduced genome, and metabolic pathways which mainly depend on exosymbiotic or exoparasitic relationships with the bacterial host, CPR microbes were found to be abundant in almost all environments. They can be considered survivors in highly competitive circumstances within microbial communities. However, their defense mechanisms and phenotypic characteristic remain poorly explored. Here, we conducted a thorough in silico analysis on 4,062 CPR genomes to search for antibiotic resistance (AR)-like enzymes using BLASTp and functional domain predictions against an exhaustive consensus AR database and conserved domain database (CDD), respectively. Our findings showed that a rich reservoir of divergent AR-like genes ( n = 30,545 hits, mean = 7.5 hits/genome [0 to 41]) were distributed across the 13 CPR superphyla. These AR-like genes encode 89 different enzymes that are associated with 14 different chemical classes of antimicrobials. Most hits found (93.6%) were linked to glycopeptide, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and aminoglycoside resistance. Moreover, two AR profiles were discerned for the Microgenomates group and " Candidatus Parcubacteria," which were distinct between them and differed from all other CPR superphyla. CPR cells seem to be active players during microbial competitive interactions; they are well equipped for microbial combat in different habitats, which ensures their natural survival and continued existence. IMPORTANCE To our knowledge, this study is one of the few studies that characterize the defense systems in the CPR group and describes the first repertoire of antibiotic resistance (AR) genes. The use of a BLAST approach with lenient criteria followed by a careful examination of the functional domains has yielded a variety of enzymes that mainly give three different mechanisms of action of resistance. Our genome analysis showed the existence of a rich reservoir of CPR resistome, which is associated with different antibiotic families. Moreover, this analysis revealed the hidden face of the reduced-genome CPR, particularly their weaponry with AR genes. These data suggest that CPR are competitive players in the microbial war, and they can be distinguished by specific AR profiles.

Candida auris is an emerging multiresistant pathogen causing nosocomial fungal infection. Specific detection and identification are necessary. Our goal is to develop a new qPCR system that enables rapid detection of C. auris, based on a GPI (glycosyl-phosphatidylinositol) protein-encoding gene. This system is reproducible and sensitive with a limit of detection of 13 C. auris CFU/qPCR reaction. The 100% specificity of this system is confirmed on 2073 clinical and environmental samples, 50 different bacterial species, and 9 Candida spp. (70 strains). This system is suitable to correctly identify C. auris infections and to trace its source.

Candida auris is an emerging multidrug-resistant yeast causing nosocomial infections and associated with high mortality in immunocompromised patients. Rapid identification and characterisation are necessary for diagnosis and containing its spread. In this study, we present a selective culture medium for all C. auris clades. This medium is sensitive with a limit of detection ranging between 10 1 and 10 2 CFU/mL. The 100% specificity of SCA (specific C. auris ) medium is confirmed on a set of 135 Candida strains, 50 bacterial species and 200 human stool samples. Thus, this medium specifically selects for C. auris isolation from clinical samples, allowing the latter to study its phenotypic profile.

Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.

Immunodepression, whether due to HIV infection or organ transplantation, has increased human vulnerability to fungal infections. These conditions have created an optimal environment for the emergence of opportunistic infections, which is concomitant to the increase in antifungal resistance. The use of conventional antifungal drugs as azoles and polyenes can lead to clinical failure, particularly in immunocompromised individuals. Difficulties related to treating fungal infections combined with the time required to develop new drugs, require urgent consideration of other therapeutic alternatives. Drug repurposing is one of the most promising and rapid solutions that the scientific and medical community can turn to, with low costs and safety advantages. To treat life-threatening resistant fungal infections, drug repurposing has led to the consideration of well-known and potential molecules as a last-line therapy. The aim of this review is to provide a summary of current antifungal compounds and their main resistance mechanisms, following by an overview of the antifungal activity of non-traditional antimicrobial drugs. We provide their eventual mechanisms of action and the synergistic combinations that improve the activity of current antifungal treatments. Finally, we discuss drug repurposing for the main emerging multidrug resistant (MDR) fungus, including the Candida auris , Aspergillus or Cryptococcus species.

Non-human primate populations act as potential reservoirs for human pathogens, including viruses, bacteria and parasites, which can lead to zoonotic infections. Furthermore, intestinal microorganisms may be pathogenic organisms to both non-human primates and humans. It is, therefore, essential to study the prevalence of these infectious agents in captive and wild non-human primates. This study aimed at showing the prevalence of the most frequently encountered human enteric protozoa in non-human primate populations based on qPCR detection. The three populations studied were common chimpanzees ( Pan troglodytes ) in Senegal and gorillas ( Gorilla gorilla ) in the Republic of the Congo and in the Beauval Zoo (France). Blastocystis spp. were mainly found, with an occurrence close to 100%, followed by Balantidium coli (23.7%), Giardia intestinalis (7.9%), Encephalitozoon intestinalis (1.3%) and Dientamoeba fragilis (0.2%). None of the following protozoa were detected: Entamoeba histolytica , Enterocytozoon bieneusi , Cryptosporidium parvum , C . hominis , Cyclospora cayetanensis or Cystoisospora belli . As chimpanzees and gorillas are genetically close to humans, it is important to monitor them frequently against different pathogens to protect these endangered species and to assess potential zoonotic transmissions to humans.

We developed a novel culture medium, referred to FastFung medium as suitable for the culture of clinical fungi, including fastidious ones, for both research and diagnostic studies. It is based on Schædler agar supplemented with many essential components for the growth of fastidious fungi. It also contains selective antibacterial agents for the inhibition of contaminant bacteria growth. In this preliminary study, the FastFung medium was compared to the gold standard Sabouraud medium for 98 fungal and 20 bacterial strains. The fungal strain positive culture rate was 100% vs. 95% and the bacterial strain inhibition was 100% vs. 20%, for the FastFung and Sabouraud media, respectively. When compared to the Sabouraud medium on 120 clinical samples, the FastFung medium displayed both a higher fungal colonies count, and a lower culture contamination rate. Storage at 4 °C for 4 weeks did not alter the FastFung culture medium performances for the six isolates of Candida, Cryptococcus, and Penicillium tested. These encouraging results suggest future development of using the FastFung medium in clinical mycology and in mycobiome characterization. Further prospective evaluation aiming at assessing whether implementing the FastFung medium in the routine workflow simplifies and strengthen fungal isolation capacities in the clinical laboratory is warranted., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Malassezia is a lipid-dependent commensal yeast of the human skin. The different culture media and skin sampling methods used to grow these fastidious yeasts are a source of heterogeneity in culture-based epidemiological study results. This study aimed to compare the performances of three methods of skin sampling, and two culture media for the detection of Malassezia yeasts by culture from the human skin. Three skin sampling methods, namely sterile gauze, dry swab, and Transwab TM with transport medium, were applied on 10 healthy volunteers at 5 distinct body sites. Each sample was further inoculated onto either the novel FastFung medium or the reference Dixon agar for the detection of Malassezia spp. by culture. At least one colony of Malassezia spp. grew on 93/300 (31%) of the cultures, corresponding to 150 samplings. The positive culture rate was 67%, 18%, and 15% ( P < 10 -3 ), for samples collected with sterile gauze, Transwab TM , and dry swab, respectively. The positive culture rate was 62% and 38% ( P < 0.003) by using the FastFung and the Dixon media, respectively. Our results showed that sterile gauze rubbing skin sampling followed by inoculation on FastFung medium should be implemented in the routine clinical laboratory procedure for Malassezia spp. cultivation.

A Gram-negative and facultative anaerobic bacterium, designated strain SN4 T , was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4 T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4 T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4 T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5 T , the phylogenetically closest neighbor and the type species of this genus. Anteiso-C 15:0 , iso-C 15:0 and C 16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4 T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4 T from G. massiliense G5 T . Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4 T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov.

Objectives: The incidence of severe filamentous fungal infections has increased over the past decade. Some of these filamentous fungi are resistant to available antifungals; it is thus urgent to find new compounds that are active against such life-threatening pathogens., Methods: In this study, 1280 drugs (Prestwick Chemical Library) were tested against six multidrug-resistant (MDR) filamentous fungi, includingAspergillus, Fusarium, Scedosporium/Lomentospora, Rhizopus and Lichtheimia species., Results: Several hits were identified that induced fungal growth inhibition ≥70%. Among the non-antifungal compounds that were effective against the clinical moulds tested in this study, clioquinol, alexidine dihydrochloride, hexachlorophene and thonzonium bromide displayed a broad activity against all strains tested., Conclusion: This study enriches the potential antifungal options that can be used against MDR invasive fungal diseases., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Blastocystis is the most common protozoan colonizing the gut of vertebrates. It modulates the human digestive microbiota in the absence of inflammation and gastrointestinal disease. Although it has been associated with human diseases, including inflammatory bowel disease, its pathogenicity remains controversial. This study aimed to assess the influence of Blastocystis on the gut bacterial communities in healthy children. We conducted a cross-sectional study on 147 Blastocystis - colonized and 149 Blastocystis - noncolonized Malian children, with Blastocystis colonization assessed by real-time PCR and gut microbial communities characterized via 16S rRNA gene (Illumina MiSeq) sequencing and bioinformatics analysis. The gut microbiota diversity was higher in Blastocystis-colonized compared to Blastocystis - noncolonized children. The phyla Firmicutes, Elusimicrobia, Lentisphaerae, and Euryarchaeota were higher in Blastocystis - colonized children, whereas Actinobacteria, Proteobacteria, unassigned bacteria, and Deinococcus-Thermus were higher in Blastocystis - noncolonized children. Moreover, Faecalibacterium prausnitzii (family Ruminococcaceae) and Roseburia sp. (family Lachnospiraceae) abundance was higher in Blastocystis-colonized children. We conclude that Blastocystis colonization is significantly associated with a higher diversity of the gut bacterial communities in healthy children, while it is not associated with the presence of potentially pathogenic bacteria in the human gut., Competing Interests: The authors declare that they have no conflict of interest.

Strain 6021061333 T was isolated from the sputum of 16-year-old girl with cystic fibrosis following a pulmonary exacerbation. This bacterial strain could not be identified by our systematic MALDI-TOF mass spectrometry screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 97.83% sequence identity with Chryseobacterium kwangjuense strain KJ1R5 T , the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. Colonies are yellow, circular and 0.5-1 mm in diameter after cultivation at 28 °C for 24 h on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 28-37 °C (optimally at 28 °C). Strain 6021061333 T is Gram-negative, non-motile and strictly aerobic bacillus. It is catalase and oxidase positive. The 4,864,678 bp-long genome, composed of five contigs, has a G+C content of 38.86%. Out of the 4427 predicted genes, 4342 were protein-coding genes and 85 were RNAs. The major fatty acids are branched (13-methyl-tetradecanoic acid and 15-methyl-hexadecenoic acid). Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of the strain 6021061333 T against genomes of the type strains of related species ranged between 23.60 and 50.40% and between 79.31 and 93.06%, respectively. According to our taxonogenomics results, we propose the creation of Chryseobacterium phocaeense sp. nov. that contains the type strain 6021061333 T (= CSUR P2660, = CECT 9670).

The use of antifungal agents in clinical settings is limited by the appearance of drug resistance and adverse side effects. There is, therefore, an urgent need to develop new drugs to strengthen the treatment of invasive fungal diseases. The aim of this study is to describe the potential repurposing of ribavirin as an adjunct therapy against Candida spp. Primary screening of a Prestwick Chemical library against Candida albicans ATCC 90028 and fluconazole-resistant Candida albicans strains was performed. Subsequently, we evaluated the responses of 100 Candida sp. strains to ribavirin, an antiviral agent, using the broth microdilution method as recommended by CLSI. We checked the involvement of efflux pump activity in the development of ribavirin resistance. We studied time-kill curves and performed a checkerboard assay for a ribavirin-antifungal combination study. Twenty-one nonstandard antifungal compounds were identified, including ribavirin. Ribavirin had antifungal activity in vitro against 63 Candida strains, including strains of C. albicans , C. parapsilosis , and C. tropicalis , with MICs ranging from 0.37 to 3.02 μg/ml, while MICs for C. krusei , C. glabrata , C. lusitaniae , and some C. albicans strains remained high (≥24.16 μg/ml). No relation was observed between efflux pump activity and ribavirin resistance. Ribavirin exhibited fungistatic activity against multidrug-resistant (MDR) C. albicans and fungicidal activity against a C. parapsilosis strain. In addition, ribavirin acted synergistically with azoles against Candida strains for which ribavirin MICs were <24.4 μg/ml. This study highlights the potential clinical application of ribavirin, alone or in association with other antifungal agents, as an adjunct anti- Candida drug., (Copyright © 2019 American Society for Microbiology.)

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-P2849 T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277 T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849 T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277 T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849 T . 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-P2849 T and strain Marseille-P3277 T 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-P2849 T (= CSUR P2849 T , = DSM 103407 T ) and Marseille-P3277 T (=CCUG 70680 T , =CSUR P3277 T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively., (© 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Culturomics has recently allowed the isolation and description of previously uncultured bacteria from the human microbiome at different body sites. As part of a project aiming to describe the human gut microbiota by culturomics, Phoenicibacter congonensis strain Marseille-P3241 T was isolated from the gut of a 45 years old Pygmy female. In the present work, we aim to describe this strain via the taxonogenomics approach. The major phenotypic, genomic and biochemical characteristics of this strain were analysed. Strain Marseille-P3241 T is an anaerobic, Gram-positive and motile coccobacillus that grows optimally at 37 °C. The genome of strain Marseille-P3241 T is 1,447,956 bp long with 43.44% GC content and its 16S rRNA gene sequence exhibited 89% sequence similarity with that of Denitrobacterium detoxificans strain NPOH1 T , the phylogenetically closest related species with current standing in nomenclature. After performing a phylogenetic and genomic analysis, we conclude that strain Marseille-P3241 T (= CCUG 70681 T  = CSUR P3241 T ) represents the type species of a new genus, for which we propose the name Phoenicibacter congonensis gen. nov., sp. nov.

Background: Although antifungals are available and usually used against fungal infections, multidrug-resistant (MDR) fungal pathogens are a growing problem for public health. Moreover, fungal infections have become more prevalent nowadays due to the increasing number of people living with immunodeficiency. Thus, previously rarely-isolated and/or unidentified fungal species including MDR yeast and moulds have emerged around the world. Recent works indicate that polymyxin antibiotics (polymyxin B and colistin) have potential antifungal proprieties. Therefore, investigating the in vitro activity of these molecules against clinical multidrug-resistant yeast and moulds could be very useful., Methods: In this study, a total of 11 MDR yeast and filamentous fungal strains commonly reported in clinical settings were tested against polymyxin antibiotics. These include strains belonging to the Candida , Cryptococcus and Rhodotorula yeast genera, along with others belonging to the Aspergillus , Fusarium , Scedosporium , Lichtheimia and Rhizopus mould genera. The fungicidal or fungistatic action of colistin against clinical yeast strains was determined by the time-kill study. Further, a checkerboard assay for its combination with antifungal agents, usually used in clinical practices (amphotericin B, itraconazole, voriconazole), was carried out against multi-drug resistant fungal strains., Results: Polymyxin B and colistin exhibited an antifungal activity against all MDR fungal strains tested with MICs ranging from 16 to 128 μg/ml, except for the Aspergillus species. In addition, colistin has a fungicidal action against yeast species, with minimum fungicidal concentrations ranging from 2 to 4 times MICs. It induces damage to the MDR Candida albicans membrane. A synergistic activity of colistin-amphotericin B and colistin-itraconazole associations against Candida albicans and Lichtheimia corymbifera strains, respectively, and colistin-fluconazole association against Rhodotorula mucilaginosa, was demonstrated using a checkerboard microdilution assay., Conclusion: colistin could be proposed, in clinical practice, in association with other antifungals, to treat life-threatening fungal infections caused by MDR yeasts or moulds., Competing Interests: Not applicable.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Intensive efforts have been made to describe the human microbiome and its involvement in health and disease. Culturomics has been recently adapted to target formerly uncultured bacteria and other unclassified bacterial species. This approach enabled us to isolate in the current study a new bacterial species, Parabacteroides timonensis strain Marseille-P3236 T , from a stool sample of a healthy 39-year-old pygmy male. This strain, is an anaerobic, gram-negative, nonspore-forming motile rod. Its genome is made up of 6,483,434 bp with 43.41% G+C content, 5046 protein-encoding genes, and 84 RNA genes. We herein provide the full description of Parabacteroides timonensis strain Marseille-P3236 T through the taxonogenomic approach., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Strain 6021052837 T was isolated from the blood culture of a hemodialysis patient on Chocolat PolyViteX medium at 37 °C after 2 days of incubation. Colonies could not be identified by our systematic MALDI-TOF Mass Spectrometry screening. The16S rRNA gene sequencing showed that the strain had 96% sequence identity with Cohnella formosensis (Genbank accession number JN806384), the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The colonies cultivated on Columbia agar with 5% sheep blood medium at 37 °C after 24 h of incubation, are white pigmented, their size varied from 1.5 to 2 mm in diameter. Strain 6021052837 T is an aerobic, Gram-negative, motile, spore forming rod, which cannot grow microaerophilically or under anaerobic conditions. The major fatty acids are branched saturated fatty acids: 14-methyl-pentadecanoic acid (34%) and 12-methyl-tetradecanoic acid (31%). The 6.328 Mb long genome, composed of 25 contigs, has a G+C content of 57.24%. Out of the 5710 predicted genes, 5646 were protein-coding genes and 64 were RNAs. A total of 3239 genes (57.37%) were assigned as putative function (by COGs) and 288 genes were identified as ORFans (5.1%). Average genomic identity of orthologous gene sequences (AGIOS) of strain 6021052837 T against genomes of the type strains of related species ranged between 58.26 and 79.63%, respectively. According to our taxonogenomics results, we propose the creation of Cohnella massiliensis sp. nov. that contains the type strain 6021052837 T (= CSUR P2659, =DSM103435).

Enterococcus timonensis sp. nov., strain Marseille-P2817 T , 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).

There is a scarcity of recent epidemiological data on intestinal parasitic infections in France. We conducted a prospective study aimed at estimating the prevalence of 10 enteric parasites in Marseille, France, using real-time polymerase chain reaction (PCR)-based diagnosis. A total of 643 faeces from 488 patients referred to the Parasitology-Mycology Laboratory of the University Hospital of Marseille over a 6 months period were included. DNA was extracted using a semi-automated method. Parasites of interest were detected using singleplex quantitative PCRs (qPCRs). For positive samples, the Blastocystis subtype was determined by sequence analysis. During the study, the overall prevalence of enteric parasites was 17%. Blastocystis sp. was the most frequent species (10.5%), followed by Dientamoeba fragilis (2.3%) and Giardia intestinalis (2.3%). The prevalence of other parasites was &lt;1% each. The ST3 Blastocystis subtype was predominant (43.6%) and the other subtypes identified were ST1, ST2, ST4 and ST6. This is the first time that a qPCR-based diagnosis has been used to survey the prevalence of 10 enteric parasites in a French University Hospital. This study confirms that fast, specific, sensitive and simultaneous detection in a single stool sample by qPCR clearly outperforms conventional microscopy-based diagnosis. Furthermore, qPCR is particularly well suited to surveying gastroenteritis agents.

Subsequent to the publication of the above article, it has been noticed that the designation of the type strain is not correct. The strain referred to throughout the article as strain AT7 T should be designated as strain Marseille-P2086 T (= CSUR P2086 T  = DSM 100837 T ). The corrected for protologue for the species Mediterraneibacter massiliensis, represented by strain Marseille-P2086 T as type strain, is given below.

An anaerobic isolate, strain AT7 T , was cultivated from a stool sample of a morbidly obese French woman using a microbial culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT7 T exhibited 96% nucleotide sequence similarity with Ruminococcus torques strain JCM 6553 T (= ATCC 27756 T  = VPI B2-51 T ), currently the closest related species with a validly published name. The strain was observed to be a Gram-stain positive, non-motile, asporogenous and coccobacillary-shaped bacterium. It was found to be catalase positive and oxidase negative. Its major fatty acids were identified as C 16:0 (54%) and C 18:1n9 (30%). The draft genome of strain AT7 T is 3,069,882 bp long with 42.4% G+C content. 2925 genes were predicted, including 2867 protein-coding genes and 58 RNAs. Based on phenotypic, biochemical, phylogenetic and genomic evidence, we propose the creation of the new genus Mediterraneibacter and species, Mediterraneibacter massiliensis, that contains strain AT7 T (= CSUR P2086 T  = DSM 100837 T ), and the reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus, Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., with type strain Eg2 T (= KCTC 5757 T  = JCM15917 T ), Mediterraneibacter lactaris comb. nov., with type strain ATCC 29176 T (= VPI X6-29 T ), Mediterraneibacter torques comb. nov., with type strain ATCC 27756 T (= VPI B2-51 T ), Mediterraneibacter gnavus comb. nov., with type strain ATCC 29149T (= VPI C7-9T) and Mediterraneibacter glycyrrhizinilyticus comb. nov., with type strain ZM35 T (= JCM 13368 T  = DSM 17593 T ), respectively.

A novel strain of a Gram-stain negative, non-motile, non-spore forming rod-shaped, obligate anaerobic bacterium, designated AT11 T , was isolated from a stool sample of a morbidly obese woman living in Marseille, France. This bacterium was characterized using biochemical, chemotaxonomic, and phylogenetic methods. The 16S rRNA gene sequence analysis showed that strain AT11 T had a 97.8% nucleotide sequence similarity with Eisenbergiella tayi strain B086562 T , the closest species with standing in nomenclature. The major cellular fatty acids of the novel isolate were C 16:0 followed by saturated or unsaturated C 18 fatty acids (C 18:1 n9, C 18:1 n5 and C 18:0) . The draft genome of strain AT11 T is 7,114,554 bp long with 48% G+C content. 6176 genes were predicted, including 6114 protein-coding genes and 62 were RNAs (with 2 5S rRNA genes, two 16S rRNA genes, two 23S rRNA genes, and 56 tRNA genes). The digital DNA-DNA hybridization (dDDH) relatedness between the new isolate and E. tayi strain B086562 T was 23.1% ± 2.2. Based on the phenotypic, chemotaxonomic, genomic, and phylogenetic characteristics, Eisenbergiella massiliensis sp. nov., is proposed. The type strain is AT11 T (= DSM 100838 T  = CSUR P2478 T ).

Eggerthella timonensis strain Marseille-P3135 is a new bacterial species, isolated from the stool sample of a healthy 8-year-old pygmy female. This strain (LT598568) showed a 16S rRNA sequence similarity of 96.95% with its phylogenetically closest species with standing in nomenclature Eggerthella lenta strain DSM 2243 (AF292375). This bacterium is a nonspore forming, Gram-positive, nonmotile rod with catalase but no oxidase activity. Its genome is 3,916,897 bp long with 65.17 mol% of G + C content. Of the 3,371 predicted genes, 57 were RNAs and 3,314 were protein-coding genes. Here, we report the main phenotypic, biochemical, and genotypic characteristics of E. timonensis strain Marseille-P3135 (=CSUR P3135, =CCUG 70327); ti.mo.nen'sis, N.L. masc. adj., with timonensis referring to La Timone, which is the name of the hospital in Marseille (France) where this work was performed). Strain is a nonmotile Gram-positive rod, unable to sporulate, oxidase negative, and catalase positive. It grows under anaerobic conditions between 25°C and 42°C but optimally at 37°C., (© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

" Nocardia suismassiliense " strain S-137 isolated from Sus scrofa feces exhibits a 9.4-Mb (67.1% GC content) draft genome sequence containing 8,658 protein-coding genes, 66 tRNAs, and 9 rRNAs. In silico DNA-DNA hybridization confirmed strain S-137 as representative of a new species, " Nocardia suismassiliense ," closely related to N. tenerifensis and N. brasiliensis ., (Copyright © 2018 Fellag et al.)

The study of the vaginal microbiota using the "culturomics concept" allowed us to isolate, from the vaginal swab of an asymptomatic 20-year-old woman who had sexual relations with another woman with bacterial vaginosis, an unknown Gram-positive anaerobic coccus-shaped bacterium that was designated strain Marseille-P2951 T and characterized using taxono-genomics. Strain Marseille-P2951 T is non-motile and non-spore forming and exhibits catalase and oxidase activities. Its 16S rRNA gene-based identification showed 98.5% identity with Ezakiella peruensis, the phylogenetically closest species. The major fatty acids are C18:1n9 (58%) and C16:0 (22%). With a 1,741,785 bp length, the G+C content of the genome is 36.69%. Of a total of 1657 genes, 1606 are protein-coding genes and 51 RNAs. Also, 1123 genes are assigned a putative function and 127 are ORFans. Phenotypic, phylogenetic, and genomics analyses revealed that strain Marseille-P2951 T (=CSUR P2951 =DSM 103122) is distinct and represents a new species of the genus Ezakiella, for which the name Ezakiella massiliensis sp. nov. is proposed.

Objective: Efficient and easy-to-use DNA extraction and purification methods are critical in implementing PCR-based diagnosis of pathogens. In order to optimize the routine clinical laboratory diagnosis of eukaryotic enteric pathogens, we compare, via quantitative PCR cycle threshold (Ct) values, the efficiency of two DNA extraction kits: the semi-automated EZ1 ® (Qiagen) and the manual QIAamp ® DNA Stool Mini Kit (Qiagen), on six protozoa: Blastocystis spp., Cryptosporidium parvum/hominis, Cyclospora cayetanensis, Dientamoeba fragilis, Giardia intestinalis and Cystoisospora belli and one microsporidia: Enterocytozoon bieneusi., Results: Whereas EZ1 ® (Qiagen) and QIAamp ® DNA Stool Mini Kit (Qiagen) yielded similar performances for the detection of Cryptosporidium spp. and D. fragilis, significant lower Ct values (p < 0.002) pointed out a better performance of EZ1 ® on the five remaining pathogens. DNA extraction using the semi-automated EZ1 ® procedure was faster and as efficient as the manual procedure in the seven eukaryotic enteric pathogens tested. This procedure is suitable for DNA extraction from stools in both clinical laboratory diagnosis and epidemiological study settings.

'Cellulomonas timonensis' sp. nov. strain sn7 T is a new species within the Cellulomonas genus. We present the main phenotypic characteristics and provide a complete annotation of its genome sequence. This facultative anaerobic bacterium, isolated from the stool of 38-year-old obese Frenchman, is Gram-positive, has motile rods and is sporulating. The genome is 4 057 828 bp long with 72.42% G + C content. Of the 3732 predicted genes, 3667 were protein-coding genes and 65 were RNAs.

Strain SIT6 T was isolated from the fecal flora of a severely malnourished child as part of a broad "culturomics" study aiming to maximize the culture conditions for the in-depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6 T shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKP T (NR&#95;029151), the phylogenetically closest type species. Colonies are creamy white, circular, 4-5 mm in diameter after cultivation at 37°C for 24 hr on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 25-56°C (optimally at 37°C). Strain SIT6 T is a gram-positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637-bp-long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein-coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA-DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6 T against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6 T (=CSUR P2452 T , =DSM 29059 T )., (© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Research on the relationship between changes in the gut microbiota and human disease, including AIDS, is a growing field. However, studies on the eukaryotic component of the intestinal microbiota have just begun and have not yet been conducted in HIV-infected patients. Moreover, eukaryotic community profiling is influenced by the use of different methodologies at each step of culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test the efficiency of each method in recovering eukaryotic DNA from fecal samples. Our results revealed that recovering eukaryotic components from fecal samples differs significantly among DNA extraction methods. Subsequently, the composition of the intestinal eukaryotic microbiota was evaluated in HIV-infected patients and healthy volunteers through clone sequencing, high-throughput sequencing of nuclear ribosomal internal transcribed spacers 1 (ITS1) and 2 (ITS2) amplicons and real-time PCRs. Our results revealed that not only richness (Chao-1 index) and alpha diversity (Shannon diversity) differ between HIV-infected patients and healthy volunteers, depending on the molecular strategy used, but also the global eukaryotic community composition, with little overlapping taxa found between techniques. Moreover, our results based on cloning libraries and ITS1/ITS2 metabarcoding sequencing showed significant differences in fungal composition between HIV-infected patients and healthy volunteers, but without distinct clusters separating the two groups. Malassezia restricta was significantly more prevalent in fecal samples of HIV-infected patients, according to cloning libraries, whereas operational taxonomic units (OTUs) belonging to Candida albicans and Candida tropicalis were significantly more abundant in fecal samples of HIV-infected patients compared to healthy subjects in both ITS subregions. Finally, real-time PCR showed the presence of Microsporidia, Giardia lamblia, Blastocystis and Hymenolepis diminuta in different proportions in fecal samples from HIV patients as compared to healthy individuals. Our work revealed that the use of different sequencing approaches can impact the perceived eukaryotic diversity results of the human gut. We also provide a more comprehensive view of the eukaryotic community in the gut of HIV-infected patients through the complementarity of the different molecular techniques used. Combining these various methodologies may provide a gold standard for a more complete characterization of the eukaryotic microbiome in future studies.

Bartonella tribocorum is a Gram-negative bacterium known to infect animals, and rodents in particular, throughout the world. In this report, we present the draft genome sequences of two strains of B. tribocorum isolated from the blood of a rodent in Laos and a shrew in Cambodia., (Copyright © 2018 Hadjadj et al.)

Herein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut.

Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972 T , could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777 T , the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The major cell fatty acids were identified as 13-methyl-tetradecanoic acid (61%), 3-hydroxy-heptadecanoic acid (16%) and 15-methyl-11-hexadecenoic acid (11%). D-glucose, D-mannose, aesculin, D-maltose, D-trehalose, and gentibiose are the main carbon source. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity values (ANI) of the strain G972 T against genomes of the type strains of related species ranged between 18.9 and 32.8% and between 71.46 and 83.61%, respectively, thus confirming again the new species status of the strain. Here, we describe the characteristics of this organism, complete genome sequence and annotation. The 5,390,132 bp size genome contains 4867 protein-coding genes, 89 RNAs (three genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 84 tRNAs) with 35.51% GC content. Finally, on the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we conclude that strain strain G972 T (= DSM 103388 T  = CSUR P2233 T ) represents a novel species for which we propose the name Chryseobacterium timonianum. The 16S rRNA and genome sequences are available in GenBank database under accession numbers LT161886 and FJVD00000000.

The proportion of cultured microorganisms is dramatically lower than those predicted to be involved in colonization, acute, or chronic infections. We report our laboratory's contribution to promoting culture methods. As a result of using culturomics in our clinical microbiology laboratories (including amoeba co-culture and shell-vial culture) and through the use of matrix-assisted laser desorption/ionization-time-of-flight and the 16S rRNA gene for identification, we cultured 329 new bacterial species. This is also the first time that 327 of species have been isolated from humans, increasing the known human bacterial repertoire by 29%. We isolated 4 archaeal species for the first time from human, including 2 new species. Of the 100 isolates of giant viruses, we demonstrated the human pathogenicity of Mimivirus in pneumonia and Marseillevirus in diverse clinical situations. From sand flies, we isolated most of the known Phlebovirus strains that potentially cause human infections. Increasing the repertoire of human-associated microorganisms through culture will allow us to test pathogenicity models with viable microorganisms., (© The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

The human gut is composed of a large diversity of microorganisms, which have been poorly described. Here, using culturomics, a new concept based on the variation in culture conditions and MALDI-TOF MS identification, we proceed to explore the microbial diversity of the complex ecosystem of the human gut. Using this approach, we isolated strain AT8 T (=CSUR P2118 =  DSM 101782) from stool specimens collected from a 51-year-old obese French woman. Strain AT8 T is a strictly anaerobic, nonmotile, nonspore-forming gram-positive coccus that do not exhibit catalase and oxidase activities. 16S rDNA-based identification of strain AT8 T demonstrated 92% gene sequence similarity with Eggerthella lenta DSM 2243, the phylogenetically closed validly named type species. Here, we present a set of features for the strain AT8 T and the description of its complete genome sequence and annotation. The 2,091,845 bp long genome has a G+C content of 63.46% and encodes1,849 predicted genes; 1,781 were protein-coding genes, and 68 were RNAs. On the basis of the characteristics reported here, we propose the creation of a new bacterial genus Hugonella gen. nov., belonging to the Eggerthellaceae family and including Hugonella massiliensis gen. nov., sp. nov., strain AT8 T as the type strain., (© 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Gastrointestinal parasite infections represent one of the biggest public health problems in the world. Therefore, appropriate innovative tools are needed for assessing interventions to control these infections. This study aims to compare the performance of real-time polymerase chain reaction (PCR) assays to microscopic examination for detection of intestinal parasites. A direct microscopic examination and stool concentration was performed on 98 stool samples from patients attending Senegalese hospitals. Negative microscopic control samples were also collected in Nice and Marseille (France). Species-specific primers/probes were used to detect 20 common gastrointestinal protozoans and helminths. Positive frequency and the sensitivity of each real-time PCR assay were compared with conventional microscopic examination. Real-time PCR was positive in 72 of 98 samples (73.5%), whereas microscopic examination was positive in 37 (37.7%) samples ( P < 0.001). The real-time PCR assays were more sensitive than microscopy, with 57.4% (31/54) versus 18.5% (10/54), respectively, in the detection of parasites in asymptomatic patients ( P < 0.05). In terms of polyparasitism, there were more coinfections detected by real-time PCR assays compared with microscopic methods (25.5% versus 3.06%). In comparison to parasite prevalence on individual samples, the results showed a perfect agreement (100%) between the two techniques for seven species, whereas discrepancies were observed for the others (agreement percentage varying from 64.2% to 98.9%). Real-time PCR appeared to be superior to microscopic examination for the detection of parasites in stool samples. This assay will be useful in diagnostic laboratories and in the field for evaluating the efficacy of mass drug administration programs.

In 1675, Antoni Van Leeuwenhoeck was the first to observe several forms using an optical microscope that he named "animalcules", realizing later that these were microorganisms. The first classification of living organisms proposed by Ehrenberg in 1833 was based on what we could visualize. The failure of this kind of classification arises from viral culture, which preceded direct observations that were finally achieved during the 20th century by electron microscopy. The number of prokaryotic species is estimated at approximately 10 million, although only 1800 were known in 1980, and 14,000 to date, thanks to the advent of 16S rRNA amplification and sequencing. This highlights our inability to access the entire diversity. Indeed, a large number of bacteria are only, known as Operational Taxonomic Units (OTUs) and detected as a result of metagenomics studies, revealing an unexplored world known as the "dark matter". Recently, the rebirth of bacterial culture through the example of culturomics has dramatically increased the human gut repertoire as well as the 18SrRNA sequencing allowed to largely extend the repertoire of Eukaryotes. Finally, filtration and co-culture on free-living protists associated with high-throughput culture elucidated a part of the megavirome. While the majority of studies currently performed on the human gut microbiota focus on bacterial diversity, it appears that several other prokaryotes (including archaea) and eukaryotic populations also inhabit this ecosystem; their detection depending exclusively on the tools used. Rational and comprehensive establishment of this ecosystem will allow the understanding of human health associated with gut microbiota and the potential to change this., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Dirofilaria immitis and D. repens are filarioid nematodes of animals and humans, transmitted by the bite of infected mosquitoes. Domestic and wild canids are a major natural host and reservoir for these parasites. In this study, we designed a duplex real-time PCR protocol targeting the mitochondrial cytochrome c oxidase subunit I (COI) gene, detecting both D. immitis and D. repens using two primer pairs and two Dirofilaria-specific hydrolysable probes. The sensitivity and specificity of the primers and probes were tested in both experimental and naturally infected samples. The detection limits of this assay were evaluated using plasmid DNA from D. immitis and D. repens. No cross-reaction was observed when testing this system against DNA from other filarial nematodes. The detection limit of the real-time PCR system was one copy per reaction mixture containing 5μl of template DNA. Field application of the new duplex real-time assay was conducted in Corsica. The prevalence rate of D. immitis was 21.3% (20/94) in dogs. In a locality where most dogs with Dirofilaria spp. infection were found, D. immitis and D. repens were detected in 5% (20/389) and 1.5% (6/389) of the Aedes albopictus population, respectively. These results suggest that this sensitive assay is a powerful tool for monitoring dirofilariosis in endemic or high risk areas., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Massilioclostridium coli strain Marseille-P2976 T (= 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-P2976 T 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.