Using culturomics, a recently developed strategy based on diversified culture conditions for the isolation of previously uncultured bacteria, we isolated strain Marseille‐P3296T from a fecal sample ...of a healthy pygmy female. A multiphasic approach, taxono‐genomics, was used to describe the major characteristics of this anaerobic and gram‐positive bacillus that is unable to sporulate and is not motile. The genome of this bacterium is 1,878,572 bp‐long with a 57.94 mol% G + C content. On the basis of these characteristics and after comparison with its closest phylogenetic neighbors, we are confident that strain Marseille‐P3296T (=CCUG 70328 = CSUR P3296) is the type strain of a novel species for which we propose the name Collinsella bouchesdurhonensis sp. nov.
Using culturomics, a recently developed strategy based on diversified culture conditions for the isolation of previously uncultured bacteria, we isolated a new species, Collinsella bouchesdurhonensis sp. nov., from a stool sample of a healthy 50‐year‐old pygmy female.
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.
Eggerthella timonensis strain Marseille‐P3135 is a new bacterial species, isolated from the stool sample of a healthy 8‐year‐old pygmy female. We are reporting here the main phenotypic, biochemical, and genotypic characteristics
Antibiotics (ABX) compromise the efficacy of programmed cell death protein 1 (PD-1) blockade in cancer patients, but the mechanisms underlying their immunosuppressive effects remain unknown. By ...inducing the down-regulation of mucosal addressin cell adhesion molecule 1 (MAdCAM-1) in the ileum, post-ABX gut recolonization by Enterocloster species drove the emigration of enterotropic α4β7 + CD4 + regulatory T 17 cells into the tumor. These deleterious ABX effects were mimicked by oral gavage of Enterocloster species, by genetic deficiency, or by antibody-mediated neutralization of MAdCAM-1 and its receptor, α4β7 integrin. By contrast, fecal microbiota transplantation or interleukin-17A neutralization prevented ABX-induced immunosuppression. In independent lung, kidney, and bladder cancer patient cohorts, low serum levels of soluble MAdCAM-1 had a negative prognostic impact. Thus, the MAdCAM-1–α4β7 axis constitutes an actionable gut immune checkpoint in cancer immunosurveillance.
Abstract
Biomarkers guiding the neoadjuvant use of immune-checkpoint blockers (ICB) are needed for patients with localized muscle-invasive bladder cancers (MIBC). Profiling tumor and blood samples, ...we found that follicular helper CD4+ T cells (TFH) are among the best therapeutic targets of pembrolizumab correlating with progression-free survival. TFH were associated with tumoral CD8 and PD-L1 expression at baseline and the induction of tertiary lymphoid structures after pembrolizumab. Blood central memory TFH accumulated in tumors where they produce CXCL13, a chemokine found in the plasma of responders only. IgG4+CD38+ TFH residing in bladder tissues correlated with clinical benefit. Finally, TFH and IgG directed against urothelium-invasive Escherichia coli dictated clinical responses to pembrolizumab in three independent cohorts. The links between tumor infection and success of ICB immunomodulation should be prospectively assessed at a larger scale.
Significance:
In patients with bladder cancer treated with neoadjuvant pembrolizumab, E. coli–specific CXCL13 producing TFH and IgG constitute biomarkers that predict clinical benefit. Beyond its role as a biomarker, such immune responses against E. coli might be harnessed for future therapeutic strategies.
This article is highlighted in the In This Issue feature, p. 2221
The aim of this study was to characterise the molecular drivers of multidrug resistance in Proteus mirabilis isolated from Algerian community and hospital patients.
A total of 166 P. mirabilis ...isolates were collected from two hospitals and eight private laboratories from four cities (Khemis Miliana, Aïn Defla, Oran and Chlef) located in northwestern Algeria. All isolates were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antimicrobial susceptibility testing was performed by the disk diffusion and Etest methods. Genes encoding AmpC β-lactamases, extended-spectrum β-lactamases (ESBLs), quinolone resistance and aminoglycoside-modifying enzymes (AMEs) as well as plasmid replicon typing were characterised by PCR. Clonal relationships were also determined by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) typing and were compared with MALDI-TOF/MS proteomic typing.
Of the 166 P. mirabilis isolates, 14 (8.4%) exhibited resistance to important antibiotics, including amoxicillin, amoxicillin/clavulanic acid, cefotaxime, gentamicin and ciprofloxacin, of which 4/14 (28.6%) had an ESBL genotype (blaCTX-M-2) and 10 (71.4%) had an AmpC/ESBL genotype (blaCMY-2/blaTEM-1). AME genes were detected in all isolates, including ant(2′′)-I, aac(3)-I, aac(6′)-Ib-cr and aac(3)-IV. The qnrA gene was identified in 13 isolates (7.8%). ERIC-PCR showed one predominant clone, with eight blaCMY-2-producing isolates from UHC Oran belonging to profile A clustering together in the MALDI-TOF/MS dendrogram.
Here we report the first description of AME and plasmid-mediated quinolone resistance genes among ESBL- and/or AmpC β-lactamase-producing P. mirabilis isolates from community- and hospital-acquired infections in northwestern Algeria.
AbstractParabacteroides massiliensis sp. nov., strain Marseille-P2231 T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It 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 9497 T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231 T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides.
AbstractThe human gastrointestinal tract exists as a complex ecosystem and contains a mycobiome and a microbiome that play central roles in host health, disease and immune system regulation. Here, we ...reviewed the traditional culture-dependent methods, the culturomics methods and the molecular methods used to study the gut mycobiome and microbiome. With the development of next-generation sequencing techniques, these last two methods have greatly broadened the understanding of the roles of gut bacteria in health and disease. Thus, dysbiosis of the gut microbiota and mycobiota has been found to be associated with some diseases; disruptions to the fungal and bacterial commensal communities influence the immune response and impact disease status.
L'établissement d'un répertoire exhaustif ainsi que son élargissement constituent les deux objectifs principaux de ce travail. Nous avons d'abord établi la toute première liste de bactéries ...identifiées par culture des voies respiratoires au travers de la littérature scientifique. Nous répertorions ici 756 espèces, ce qui représente 27,23% de l'ensemble des bactéries isolées chez l'homme lorsque comparé au répertoire établi récemment par Bilen et al. Parmi ces bactéries, 514 avaient déjà été isolées au moins une fois dans les poumons. Plus de la moitié (i.e., 65,5%) des bactéries isolées pour la première fois dans des échantillons de poumons, ont été identifiées après les années 2000, soulignant la nécessité de poursuivre les efforts pour cultiver des microbes à partir des échantillons de voies respiratoires. Nous pensons que la combinaison de méthodes de culture à grande échelle telles que la culturomique et la métagénomique aidera à mieux décrire le microbiote pulmonaire. Des études antérieures sur le microbiote digestif le démontre. Nous avons ensuite utilisé des approches culturomiques et métagénomiques pour explorer le microbiote respiratoire d'individus sains. Nous avons isolé 193 bactéries par culturomics. Parmi ceux-ci, nous avons ajouté 84 au répertoire du microbiote respiratoire, dont 14 nouvelles espèces. En utilisant des approches métagénomiques, 139 OTU identifiées au rang de l'espèce dont seulement 49 (17,3%) étaient également retrouvées par culturomique, confortant la complémentarité des deux approches. Enfin, nous avons utilisé la taxonogénomique, une nouvelle approche permettant la description de nouvelles espèces bactériennes, pour décrire 19 bactéries.
The establishment of a comprehensive directory and its expansion through the use of high-speed culture methods are the two main objectives of this thesis work. We first established the first list of bacteria identified by airway culture through the scientific literature. Here we list 756 species, representing 27.23% of all bacteria isolated from humans when compared to the recently established repertoire of Bilen et al. Of these bacteria, 514 had already been isolated at least once in the lungs. Considering bacteria isolated for the first time in lung samples, more than half (ie, 65.5%) were identified after the 2000s, highlighting the need for continued efforts to grow microbes from lane samples respiratory. We believe that the combination of large scale culture methods such as culturomics and metagenomics will help to better describe the pulmonary microbiota. Previous studies on the digestive microbiota have shown the complementarity of these two approaches. We then used culturomic and metagenomic approaches to explore the respiratory microbiota of healthy individuals. We isolated 193 bacteria by culturomics. Of these, we added 84 bacteria to the repertoire of the respiratory microbiota, including 14 new species discovered. Using metagenomic approaches, 139 OTUs identified with the rank of the species of which only 49 (17.3%) were also recovered by culturomics, reinforcing the complementarity of the two approaches. Finally, we used taxonogenomics, a new approach for describing new bacterial species by integrating genomic and proteomic data with those that are classically integrated. Using this approach, 19 bacteria were described as part of this work.
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