A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

AbstractBackgroundAnalysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. Unfortunately, there is no such reference database available for the vaginal microbiome.ResultsIn this study, we assembled a comprehensive human vaginal non-redundant gene catalog (VIRGO) from 264 vaginal metagenomes and 416 genomes of urogenital bacterial isolates. VIRGO includes 0.95 million non-redundant genes compiled from a total of 5.5 million genes belonging to 318 unique bacterial species. We show that VIRGO covers more than 95% of the vaginal bacterial gene content in metagenomes from North American, African, and Chinese women. The gene catalog was extensively functionally annotated from 17 diverse protein databases, and importantly taxonomy was assigned through in silico binning of genes derived from metagenomic assemblies. To further enable focused analyses of individual genes and proteins, we also clustered the non-redundant genes into vaginal orthologous groups (VOG). The gene-centric design of VIRGO and VOG provides an easily accessible tool to comprehensively characterize the structure and function of vaginal metagenome and metatranscriptome datasets. To highlight the utility of VIRGO, we analyzed 1,507 additional vaginal metagenomes, uncovering an as of yet undetected high degree of intraspecies diversity within and across vaginal microbiota.ConclusionsVIRGO offers a convenient reference database and toolkit that will facilitate a more in-depth understanding of the role of vaginal microorganisms in women’s health and reproductive outcomes.

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A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab009 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Marianne Borderes ◽

Cyrielle Gasc ◽

Emmanuel Prestat ◽

Mariana Galvão Ferrarini ◽

Susana Vinga ◽

...

Keyword(s):

Gut Microbiota ◽

Comprehensive Evaluation ◽

Species Level ◽

Human Gut ◽

Trade Off ◽

Microbial Species ◽

Gene Catalog ◽

Redundant Gene ◽

Assessment Metrics ◽

Functional Analyses

Abstract The human gut microbiota performs functions that are essential for the maintenance of the host physiology. However, characterizing the functioning of microbial communities in relation to the host remains challenging in reference-based metagenomic analyses. Indeed, as taxonomic and functional analyses are performed independently, the link between genes and species remains unclear. Although a first set of species-level bins was built by clustering co-abundant genes, no reference bin set is established on the most used gut microbiota catalog, the Integrated Gene Catalog (IGC). With the aim to identify the best suitable method to group the IGC genes, we benchmarked nine taxonomy-independent binners implementing abundance-based, hybrid and integrative approaches. To this purpose, we designed a simulated non-redundant gene catalog (SGC) and computed adapted assessment metrics. Overall, the best trade-off between the main metrics is reached by an integrative binner. For each approach, we then compared the results of the best-performing binner with our expected community structures and applied the method to the IGC. The three approaches are distinguished by specific advantages, and by inherent or scalability limitations. Hybrid and integrative binners show promising and potentially complementary results but require improvements to be used on the IGC to recover human gut microbial species.

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Immunohistochemical identification of the pacemaker cajal cells in the normal human vagina

Archives of Gynecology and Obstetrics ◽

10.1007/s00404-005-0725-3 ◽

2005 ◽

Vol 272 (1) ◽

pp. 13-16 ◽

Cited By ~ 12

Author(s):

Ahmed Shafik ◽

Olfat El-Sibai ◽

Ismail Shafik ◽

Ali A. Shafik

Keyword(s):

Cajal Cells ◽

Human Vagina ◽

Normal Human ◽

Immunohistochemical Identification

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Characterization of Gnomoniopsis idaeicola, the Causal Agent of Canker and Wilting of Blackberry in Serbia

Plant Disease ◽

10.1094/pdis-03-18-0516-re ◽

2019 ◽

Vol 103 (2) ◽

pp. 249-258 ◽

Cited By ~ 1

Author(s):

Miloš Stevanović ◽

Danijela Ristić ◽

Svetlana Živković ◽

Goran Aleksić ◽

Ivana Stanković ◽

...

Keyword(s):

Disease Incidence ◽

Initial Step ◽

First Record ◽

Wide Distribution ◽

Causal Agent ◽

Control Measures ◽

Molecular Features ◽

Intraspecies Diversity ◽

Specific Symptoms

Blackberry cane diseases with the symptoms of necrosis, canker, and wilting are caused by several fungi worldwide. Surveys conducted from 2013 to 2016 in Serbia revealed the occurrence of Gnomoniopsis idaeicola, the causal agent of cane canker and wilting, which was found to be distributed in almost half of the surveyed orchards, in three blackberry cultivars, and with disease incidence of up to 80%. Wide distribution and high disease incidence suggest that G. idaeicola has been present in Serbia for some time. Out of 427 samples, a total of 65 G. idaeicola isolates were obtained (isolation rate of 34.19%). Reference isolates, originating from different localities, were conventionally and molecularly identified and characterized. G. idaeicola was detected in single and mixed infections with fungi from genera Paraconiothyrium, Colletotrichum, Diaporthe, Botryosphaeria, Botrytis, Septoria, Neofusicoccum, and Discostroma, and no diagnostically specific symptoms could be related directly to the G. idaeicola infection. In orchards solely infected with G. idaeicola, blackberry plant mortality was up to 40%, and yield loses were estimated at 50%. G. idaeicola isolates included in this study demonstrated intraspecies diversity in morphological, biological, pathogenic, and molecular features, which indicates that population in Serbia may be of different origin. This is the first record of a massive outbreak of G. idaeicola infection, illustrating its capability of harmful influence on blackberry production. This study represents the initial step in studying G. idaeicola as a new blackberry pathogen in Serbia, aiming at developing efficient control measures.

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A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Journal of Bacteriology ◽

10.1128/jb.01202-08 ◽

2008 ◽

Vol 191 (1) ◽

pp. 91-99 ◽

Cited By ~ 115

Author(s):

Marc Deloger ◽

Meriem El Karoui ◽

Marie-Agnès Petit

Keyword(s):

Dna Sequences ◽

Dna Content ◽

Core Genome ◽

Biological Diversity ◽

Bacterial Species ◽

Genomic Distance ◽

The Core ◽

Intraspecies Diversity ◽

Genome Level ◽

Definition Of

ABSTRACT The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

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Biological properties and production of bacteriocins‐like‐inhibitory substances by Lactobacillus sp. strains from human vagina

Journal of Applied Microbiology ◽

10.1111/jam.14164 ◽

2019 ◽

Vol 126 (5) ◽

pp. 1541-1550 ◽

Cited By ~ 8

Author(s):

V. Fuochi ◽

V. Cardile ◽

G. Petronio Petronio ◽

P. M. Furneri

Keyword(s):

Biological Properties ◽

Human Vagina

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LACTIC ACID BACTERIA IN FOOD AND HEALTH: A REVIEW WITH SPECIAL REFERENCE TO ENTEROPATHOGENIC ESCHERICHIA COLI AS WELL AS CERTAIN ENTERIC DISEASES AND THEIR TREATMENT WITH ANTIBIOTICS AND LACTOBACILLI1

Journal of Milk and Food Technology ◽

10.4315/0022-2747-35.12.691 ◽

1972 ◽

Vol 35 (12) ◽

pp. 691-702 ◽

Cited By ~ 65

Author(s):

W. E. Sannine ◽

K. S. Muralidhara ◽

P. R. Elliker ◽

D. C. England

Keyword(s):

Escherichia Coli ◽

Lactic Acid ◽

Lactic Acid Bacteria ◽

Animal Feed ◽

Large Population ◽

Intestinal Bacteria ◽

Transfer Factors ◽

Enteric Diseases ◽

Human Vagina ◽

Vaginal Disease

Recent literature concerning enteropathogenesis and drug resistance transfer factors in Escherichia coli are summarized as well as related papers concerning the use of antibiotics in animal feed. E. coli infection in swine (colibacillosis) also is considered, especially citations indicating the similarity between the disease in man and animals. The role of intestinal bacteria in human health is reviewed, emphasizing the importance of (a) a maintained balance of organisms in the adult, (b) breast feeding in infants to establish a large population of bifidobacteria and (c) the presence of Lactobacillus organisms to maintain healthful conditions in the human vagina. The use of Lactobacillus organisms in intestinal and vaginal disease therapy is reviewed as well as the important ecological role that lactic acid bacteria play in the natural scheme where man is concerned.

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Expression and Distribution of Cyclic AMP- and Cyclic GMP-Binding Protein Kinases in the Human Vagina— An Immunohistochemical Study

Journal of Sexual Medicine ◽

10.1111/j.1743-6109.2009.01539.x ◽

2010 ◽

Vol 7 (2) ◽

pp. 888-895 ◽

Cited By ~ 4

Author(s):

Stefan Ückert ◽

Eginhard S. Waldkirch ◽

Knut Albrecht ◽

Julia Sonnenberg ◽

Kristina Langnäse ◽

...

Keyword(s):

Cyclic Amp ◽

Protein Kinases ◽

Cyclic Gmp ◽

Immunohistochemical Study ◽

Binding Protein ◽

Human Vagina

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Rate of decrease of glutamyltransferase and acid phosphatase activities in the human vagina after coitus.

Clinical Chemistry ◽

10.1093/clinchem/26.2.254 ◽

1980 ◽

Vol 26 (2) ◽

pp. 254-257 ◽

Cited By ~ 7

Author(s):

W F Gohara

Keyword(s):

Acid Phosphatase ◽

Buccal Cavity ◽

Prostatic Acid Phosphatase ◽

Healthy Human ◽

Gamma Glutamyltransferase ◽

Phosphatase Activities ◽

Gamma Glutamyl ◽

Healthy Women ◽

Human Vagina

Abstract I studied the rate at which gamma-glutamyltransferase (EC 2.3.2.2) and acid phosphatase (EC 3.1.3.2) activities decrease in the healthy human vagina after coitus. Specimens from the coital and non-coital vagina, and from the rectum and buccal cavity, and pre-ejaculate lubricating fluid were also assayed for both enzymes. Prostatic acid phosphatase was determined with use of two substrates: thymolphthalein monophosphate and alpha-naphthyl phosphate (tartrate-inhibitable fraction). Glutamyltransferase was assayed with gamma-glutamyl-p-nitroanilide as substrate. All non-coital specimens were negative for glutamyltransferase activity; the activity of acid phosphatase varied with type of substrate and type of specimen. The equation y = a + (b/x) describes the decline in activity (y) of either acid phosphatase or glutamyltransferase in the vagina of healthy women post-coitally with time (x).

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Molecular Mechanism ofN,N-Dimethylformamide Degradation inMethylobacteriumsp. Strain DM1

Applied and Environmental Microbiology ◽

10.1128/aem.00275-19 ◽

2019 ◽

Vol 85 (12) ◽

Cited By ~ 8

Author(s):

Xinyu Lu ◽

Weiwei Wang ◽

Lige Zhang ◽

Haiyang Hu ◽

Ping Xu ◽

...

Keyword(s):

Molecular Mechanisms ◽

Gene Clusters ◽

Sole Source ◽

Human Beings ◽

Sequencing Data ◽

Carbon And Nitrogen ◽

Redundant Genes ◽

Evolutionary Advantage ◽

Redundant Gene ◽

Phenotype Identification

ABSTRACTN,N-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified asMethylobacteriumsp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation byMethylobacterium.IMPORTANCEDMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader,Methylobacteriumsp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes ofMethylobacterium.

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