Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer.

Immune checkpoint blockade has emerged as a promising form of cancer therapy. However, only some patients respond to checkpoint inhibitors, while a significant proportion of patients do not, calling for the discovery of reliable biomarkers. Recent studies reported the importance of the gut microbiome in the clinical response to PD-1 blockade against advanced non-small cell lung cancer (NSCLC), highlighting Akkermansia muciniphila as a candidate biomarker.

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.

Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing.

sp. nov. (formerly genomic species 3) and sp. nov. (formerly genomic species 8) isolated from female urinary microbiome.

During an ongoing female urinary microbiome research study, strains c17Ua_112 and c31Ua_26 isolated from urine samples of a patient diagnosed with overactive bladder and a healthy postmenopausal woman, respectively, could not be allocated to any species with valid names. In this work, we aimed to characterize these strains. The 16S rRNA gene sequences confirmed that these strains are members of the genus .

Expanding the Bacterial Diversity of the Female Urinary Microbiome: Description of Eight New Species.

The genus is frequently found in the female urinary microbiome (FUM). In-depth characterization of at the species level has been barely exploited. During ongoing FUM research studies, eight strains (c8Ua_144, c8Ua_172, c8Ua_174, c8Ua_181, c9Ua_112, c19Ua_109, c19Ua_121, and c21Ua_68) isolated from urine samples of healthy women or diagnosed with overactive bladder could not be allocated to any valid species.

Urinary Microbiome of Reproductive-Age Asymptomatic European Women.

The knowledge of bacterial species diversity within the female urinary microbiome (FUM) is essential for understanding the role of the FUM in urinary tract health and disease. This study aimed to characterize the bacterial species diversity of the FUM of asymptomatic reproductive-age European women by combining extended culturomics and long-read sequencing of the near-full-length 16S rRNA gene. A total of 297 bacterial species (median of 53 species/sample) were identified, yet only 22% of the species were detected by both culture and sequencing methods.

Genomic diversity of genus .

The genus (formerly ) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of showed misidentification of some strains deposited in public databases and existence of putative novel species.

The Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Lineages.

Since the discovery of the urinary microbiome, including the identification of in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of ( = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage.

Phylogenomic analysis of a highly virulent Escherichia coli ST83 lineage with potential animal-human transmission.

The presence of specific virulence features conditions severe forms of urinary tract disease, but the frequency and distribution of these highly virulent extraintestinal pathogenic Escherichia coli strains in animals and humans is unclear. We used whole genome sequencing, comparative genomics, histological and clinical data to characterize the genetic basis for pathogenesis and origin of E. coli Ec_151217, a strain (B2, ST83, O83:H5:K5) that caused an extremely aggressive upper urinary tract infection (UTI) in a cat.

sp. nov. and sp. nov. isolated from urine of healthy women.

Two Gram-stain-positive strains, c9Ua_26_M and c11Ua_112_M, were isolated from voided urine samples from two healthy women. Comparative 16S rRNA gene sequences demonstrated that these novel strains were members of the genus . Phylogenetic analysis based on gene sequences and core genomes showed that each strain formed a separated branch and are closest to DSM 5837.

Long-term stability of the urogenital microbiota of asymptomatic European women.

Background: To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.

MicroMundo@UPorto: an experimental microbiology project fostering student's antimicrobial resistance awareness and personal and social development.

Antimicrobial resistance (AMR) is a global societal challenge requiring the contribution of professionals along with general community citizens for their containment. Portugal is one of the European countries where a lack of knowledge on the correct use of antimicrobials and AMR problematic is preeminent. Moreover, youth demotivation to pursue science careers is emerging.

The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield.

Background: In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species.

The status of the species Dicks . 2000. Request for an opinion.

During a recent study on members of the genus we realized that cultures of TV 1018 (=DSM 13171=ATCC 700934) are no longer available from the online catalogue of the German Collection of Microorganisms and Cell Cultures GmbH, being displayed as at the American Type Culture Collection. Based on data currently available, the organism deposited as ATCC 700934 is a member of the species subs. .

sp. nov., a new species of group.

One Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, and coccobacilli-shaped strain, designated c10Ua161M, was isolated from a urine sample from a reproductive-age healthy woman. Comparative 16S rRNA gene sequence analysis indicated that strain c10Ua161M belonged to the genus . Phylogenetic analysis based on and gene sequences strongly supported a clade encompassing strains c10Ua161M and eight other strains from public databases, distinct from currently recognized species of the genus Average Nucleotide Identity (ANI) and Genome-to-Genome Distance Calculator (GGDC), showed 87.