scholarly journals Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment

2021 ◽  
Vol 87 (8) ◽  
Author(s):  
Leonardo Mancabelli ◽  
Walter Mancino ◽  
Gabriele Andrea Lugli ◽  
Christian Milani ◽  
Alice Viappiani ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Vaginal Microbiota ◽  
Microbial Consortia ◽  
Microbial Composition ◽  
Vaginal Infections ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Lactobacillus Crispatus ◽  
Vaginal Tract

ABSTRACT The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxon composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results, we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated 15 L. crispatus strains from different environments in which this species abounds, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study revealed a genetic adaptation of strains to their respective ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains, together with a synthetic vaginal microbiota, reveal how this species is able to modulate the composition of the vaginal microbial consortia at the strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. IMPORTANCE The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus strains is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genomes of new L. crispatus strains from different environments, and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.

scholarly journals In VitroActivity of Glucosinolates and Their Degradation Products against Brassica-Pathogenic Bacteria and Fungi

2014 ◽  
Vol 81 (1) ◽  
pp. 432-440 ◽  
Author(s):  
T. Sotelo ◽  
M. Lema ◽  
P. Soengas ◽  
M. E. Cartea ◽  
P. Velasco
Keyword(s):  
Pseudomonas Syringae ◽  
Xanthomonas Campestris ◽  
Pathogenic Bacteria ◽  
Degradation Products ◽  
Allyl Isothiocyanate ◽  
Leaf Extracts ◽  
Soil Pathogens ◽  
Content Type ◽  
Positive Effects

ABSTRACTGlucosinolates (GSLs) are secondary metabolites found inBrassicavegetables that confer on them resistance against pests and diseases. Both GSLs and glucosinolate hydrolysis products (GHPs) have shown positive effects in reducing soil pathogens. Information about theirin vitrobiocide effects is scarce, but previous studies have shown sinigrin GSLs and their associated allyl isothiocyanate (AITC) to be soil biocides. The objective of this work was to evaluate the biocide effects of 17 GSLs and GHPs and of leaf methanolic extracts of different GSL-enrichedBrassicacrops on suppressingin vitrogrowth of two bacterial (Xanthomonas campestrispv. campestris andPseudomonas syringaepv. maculicola) and two fungal (AlternariabrassicaeandSclerotiniascletoriorum)Brassicapathogens. GSLs, GHPs, and methanolic leaf extracts inhibited the development of the pathogens tested compared to the control, and the effect was dose dependent. Furthermore, the biocide effects of the different compounds studied were dependent on the species and race of the pathogen. These results indicate that GSLs and their GHPs, as well as extracts of differentBrassicaspecies, have potential to inhibit pathogen growth and offer new opportunities to study the use ofBrassicacrops in biofumigation for the control of multiple diseases.

scholarly journals Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4538
Author(s):  
Scarlett Puebla-Barragan ◽  
Emiley Watson ◽  
Charlotte van der Veer ◽  
John A. Chmiel ◽  
Charles Carr ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Metabolic Pathways ◽  
Vaginal Microbiota ◽  
Comparative Genome Analysis ◽  
Genetic Traits ◽  
Lactobacillus Crispatus ◽  
Vaginal Swabs ◽  
The Common ◽  
Synthesis And Degradation

Lactobacillus crispatus is the dominant species in the vagina of many women. With the potential for strains of this species to be used as a probiotic to help prevent and treat dysbiosis, we investigated isolates from vaginal swabs with Lactobacillus-dominated and a dysbiotic microbiota. A comparative genome analysis led to the identification of metabolic pathways for synthesis and degradation of three major biogenic amines in most strains. However, targeted metabolomic analysis of the production and degradation of biogenic amines showed that certain strains have either the ability to produce or to degrade these compounds. Notably, six strains produced cadaverine, one produced putrescine, and two produced tyramine. These biogenic amines are known to raise vaginal pH, cause malodour, and make the environment more favourable to vaginal pathogens. In vitro experiments confirmed that strains isolated from women with a dysbiotic vaginal microbiota have higher antimicrobial effects against the common urogenital pathogens Escherichia coli and Enterococcus faecium. The results indicate that not all L. crispatus vaginal strains appear suitable for probiotic application and the basis for selection should not be only the overall composition of the vaginal microbiota of the host from which they came, but specific biochemical and genetic traits.

scholarly journals Factors Influencing the Microbial Composition of Metalworking Fluids and Potential Implications for Machine Operator's Lung

2011 ◽  
Vol 78 (1) ◽  
pp. 34-41 ◽  
Author(s):  
Jean-Benjamin Murat ◽  
Frédéric Grenouillet ◽  
Gabriel Reboux ◽  
Emmanuelle Penven ◽  
Adam Batchili ◽  
...  
Keyword(s):  
Metal Cutting ◽  
Hypersensitivity Pneumonitis ◽  
Environmental Parameters ◽  
Metalworking Fluids ◽  
Microbial Composition ◽  
Gram Positive ◽  
Gram Negative ◽  
Content Type ◽  
Kinetics Of

ABSTRACTHypersensitivity pneumonitis, also known as “machine operator's lung” (MOL), has been related to microorganisms growing in metalworking fluids (MWFs), especiallyMycobacterium immunogenum. We aimed to (i) describe the microbiological contamination of MWFs and (ii) look for chemical, physical, and environmental parameters associated with variations in microbiological profiles. We microbiologically analyzed 180 MWF samples from nonautomotive plants (e.g., screw-machining or metal-cutting plants) in the Franche-Comté region in eastern France and 165 samples from three French automotive plants in which cases of MOL had been proven. Our results revealed two types of microbial biomes: the first was from the nonautomotive industry, showed predominantly Gram-negative rods (GNR), and was associated with a low risk of MOL, and the second came from the automotive industry that was affected by cases of MOL and showed predominantly Gram-positive rods (GPR). Traces ofM. immunogenumwere sporadically detected in the first type, while it was highly prevalent in the automotive sector, with up to 38% of samples testing positive. The use of chromium, nickel, or iron was associated with growth of Gram-negative rods; conversely, growth of Gram-positive rods was associated with the absence of these metals. Synthetic MWFs were more frequently sterile than emulsions. Vegetable oil-based emulsions were associated with GNR, while mineral ones were associated with GPR. Our results suggest that metal types and the nature of MWF play a part in MWF contamination, and this work shall be followed by furtherin vitrosimulation experiments on the kinetics of microbial populations, focusing on the phenomena of inhibition and synergy.

scholarly journals Is Staphylococcus lugdunensis Significant in Clinical Samples?

2017 ◽  
Vol 55 (11) ◽  
pp. 3167-3174 ◽  
Author(s):  
Xavier Argemi ◽  
Yves Hansmann ◽  
Philippe Riegel ◽  
Gilles Prévost
Keyword(s):  
Pathogenic Bacteria ◽  
Clinical Manifestations ◽  
Clinical Samples ◽  
Opportunistic Pathogens ◽  
Coagulase Negative Staphylococci ◽  
Staphylococcus Lugdunensis ◽  
Content Type ◽  
Severe Infections ◽  
Microbiological Data

ABSTRACTThe implication of coagulase-negative staphylococci in human diseases is a major issue, particularly in hospital settings wherein these species often act as opportunistic pathogens. In addition, some coagulase-negative staphylococci such asS. lugdunensishave emerged as pathogenic bacteria, implicated in severe infections, particularly, osteoarticular infections, foreign-body-associated infections, bacteremia, and endocarditis.In vitrostudies have shown the presence of several putative virulence factors such as adhesion factors, biofilm production, and proteolytic factors that might explain clinical manifestations. Taken together, the clinical and microbiological data might change the way clinicians and microbiologists look atS. lugdunensisin clinical samples.

scholarly journals Identification and Regulation of a Novel Citrobacter rodentium Gut Colonization Fimbria (Gcf)

2015 ◽  
Vol 197 (8) ◽  
pp. 1478-1491 ◽  
Author(s):  
Gustavo G. Caballero-Flores ◽  
Matthew A. Croxen ◽  
Verónica I. Martínez-Santos ◽  
B. Brett Finlay ◽  
José L. Puente
Keyword(s):  
Escherichia Coli ◽  
Intestinal Epithelium ◽  
Pathogenic Bacteria ◽  
Critical Role ◽  
Growth Conditions ◽  
Citrobacter Rodentium ◽  
Content Type ◽  
Gut Colonization ◽  
Successful Infection

ABSTRACTThe Gram-negative enteric bacteriumCitrobacter rodentiumis a natural mouse pathogen that has been extensively used as a surrogate model for studying the human pathogens enteropathogenic and enterohemorrhagicEscherichia coli. All three pathogens produce similar attaching and effacing (A/E) lesions in the intestinal epithelium. During infection, these bacteria employ surface structures called fimbriae to adhere and colonize the host intestinal epithelium. ForC. rodentium, the roles of only a small number of its genome-carried fimbrial operons have been evaluated. Here, we report the identification of a novelC. rodentiumcolonization factor, calledgutcolonizationfimbria (Gcf), which is encoded by a chaperone-usher fimbrial operon. AgcfAmutant shows a severe colonization defect within the first 10 days of infection. Thegcfpromoter is not active inC. rodentiumunder severalin vitrogrowth conditions; however, it is readily expressed in aC. rodentiumΔhns1mutant lacking the closest ortholog of theEscherichia colihistone-like nucleoid structuring protein (H-NS) but not in mutants with deletion of the other four genes encoding H-NS homologs. H-NS binds to the regulatory region ofgcf, further supporting its direct role as a repressor of thegcfpromoter that starts transcription 158 bp upstream of the start codon of its first open reading frame. Thegcfoperon possesses interesting novel traits that open future opportunities to expand our knowledge of the structure, regulation, and function during infection of these important bacterial structures.IMPORTANCEFimbriae are surface bacterial structures implicated in a variety of biological processes. Some have been shown to play a critical role during host colonization and thus in disease. Pathogenic bacteria possess the genetic information for an assortment of fimbriae, but their function and regulation and the interplay between them have not been studied in detail. This work provides new insights into the function and regulation of a novel fimbria called Gcf that is important for early establishment of a successful infection byC. rodentiumin mice, despite being poorly expressed underin vitrogrowth conditions. This discovery offers an opportunity to better understand the individual role and the regulatory mechanisms controlling the expression of specific fimbrial operons that are critical during infection.

scholarly journals Bacterial Enzymes Catalyzing the Synthesis of 1,8-Dihydroxynaphthalene, a Key Precursor of Dihydroxynaphthalene Melanin, fromSorangium cellulosum

2018 ◽  
Vol 84 (9) ◽  
Author(s):  
Yusuke Sone ◽  
Shuto Nakamura ◽  
Makoto Sasaki ◽  
Fumihito Hasebe ◽  
Seung-Young Kim ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Optical Purity ◽  
Brown Pigment ◽  
Type I ◽  
Enzymatic System ◽  
Type Iii Polyketide Synthase ◽  
Content Type ◽  
Type Iii ◽  
Bacterial Origin

ABSTRACT1,8-Dihydroxynaphthalene (1,8-DHN) is a key intermediate in the biosynthesis of DHN melanin, which is specific to fungi. In this study, we characterized the enzymatic properties of the gene products of an operon consisting ofsoceCHS1,bdsA, andbdsBfrom the Gram-negative bacteriumSorangium cellulosum. Heterologous expression ofsoceCHS1,bdsA, andbdsBinStreptomyces coelicolorcaused secretion of a dark-brown pigment into the broth. High-performance liquid chromatography (HPLC) analysis of the broth revealed that the recombinant strain produced 1,8-DHN, indicating that the operon encoded a novel enzymatic system for the synthesis of 1,8-DHN. Simultaneous incubation of the recombinant SoceCHS1, BdsA, and BdsB with malonyl-coenzyme A (malonyl-CoA) and NADPH resulted in the synthesis of 1,8-DHN. SoceCHS1, a type III polyketide synthase (PKS), catalyzed the synthesis of 1,3,6,8-tetrahydroxynaphthalene (T4HN)in vitro. T4HN was in turn converted to 1,8-DHN by successive steps of reduction and dehydration, which were catalyzed by BdsA and BdsB. BdsA, which is a member of the aldo-keto reductase (AKR) superfamily, catalyzed the reduction of T4HN and 1,3,8-tetrahydroxynaphthalene (T3HN) to scytalone and vermelone, respectively. The stereoselectivity of T4HN reduction by BdsA occurred on thesi-face to give (R)-scytalone with more than 99% optical purity. BdsB, a SnoaL2-like protein, catalyzed the dehydration of scytalone and vermelone to T3HN and 1,8-DHN, respectively. The fungal pathway for the synthesis of 1,8-DHN is composed of a type I PKS, naphthol reductases of the short-chain dehydrogenase/reductase (SDR) superfamily, and scytalone dehydratase (SD). These findings demonstrated 1,8-DHN synthesis by novel enzymes of bacterial origin.IMPORTANCEAlthough the DHN biosynthetic pathway was thought to be specific to fungi, we discovered novel DHN synthesis enzymes of bacterial origin. The biosynthesis of bacterial DHN utilized a type III PKS for polyketide synthesis, an AKR superfamily for reduction, and a SnoaL2-like NTF2 superfamily for dehydration, whereas the biosynthesis of fungal DHN utilized a type I PKS, SDR superfamily enzyme, and SD-like NTF2 superfamily. Surprisingly, the enzyme systems comprising the pathway were significantly different from each other, suggesting independent, parallel evolution leading to the same biosynthesis. DHN melanin plays roles in host invasion and adaptation to stress in pathogenic fungi and is therefore important to study. However, it is unclear whether DHN biosynthesis occurs in bacteria. Importantly, we did find that bacterial DHN biosynthetic enzymes were conserved among pathogenic bacteria.

scholarly journals Disruption of VirB6 Paralogs in Anaplasma phagocytophilum Attenuates Its Growth

2020 ◽  
Vol 202 (23) ◽  
Author(s):  
Francy L. Crosby ◽  
Ulrike G. Munderloh ◽  
Curtis M. Nelson ◽  
Michael J. Herron ◽  
Anna M. Lundgren ◽  
...  
Keyword(s):  
Anaplasma Phagocytophilum ◽  
Pathogenic Bacteria ◽  
Tandem Repeats ◽  
Model Systems ◽  
Accession Number ◽  
Secretion Systems ◽  
Altered Expression ◽  
Content Type ◽  
Obligate Intracellular

ABSTRACT Many pathogenic bacteria translocate virulence factors into their eukaryotic hosts by means of type IV secretion systems (T4SS) spanning the inner and outer membranes. Genes encoding components of these systems have been identified within the order Rickettsiales based upon their sequence similarities to other prototypical systems. Anaplasma phagocytophilum strains are obligate intracellular, tick-borne bacteria that are members of this order. The organization of these components at the genomic level was determined in several Anaplasma phagocytophilum strains, showing overall conservation, with the exceptions of the virB2 and virB6 genes. The virB6 loci are characterized by the presence of four virB6 copies (virB6-1 through virB6-4) arranged in tandem within a gene cluster known as the sodB-virB operon. Interestingly, the virB6-4 gene varies significantly in length among different strains due to extensive tandem repeats at the 3′ end. To gain an understanding of how these enigmatic virB6 genes function in A. phagocytophilum, we investigated their expression in infected human and tick cells. Our results show that these genes are expressed by A. phagocytophilum replicating in both cell types and that VirB6-3 and VirB6-4 proteins are surface exposed. Analysis of an A. phagocytophilum mutant carrying the Himar1 transposon within the virB6-4 gene demonstrated that the insertion not only disrupted its expression but also exerted a polar effect on the sodB-virB operon. Moreover, the altered expression of genes within this operon was associated with the attenuated in vitro growth of A. phagocytophilum in human and tick cells, indicating the importance of these genes in the physiology of this obligate intracellular bacterium in such different environments. IMPORTANCE Knowledge of the T4SS is derived from model systems, such as Agrobacterium tumefaciens. The structure of the T4SS in Rickettsiales differs from the classical arrangement. These differences include missing and duplicated components with structural alterations. Particularly, two sequenced virB6-4 genes encode unusual C-terminal structural extensions resulting in proteins of 4,322 (GenBank accession number AGR79286.1) and 9,935 (GenBank accession number ANC34101.1>) amino acids. To understand how the T4SS is used in A. phagocytophilum, we describe the expression of the virB6 paralogs and explore their role as the bacteria replicate within its host cell. Conclusions about the importance of these paralogs for colonization of human and tick cells are supported by the deficient phenotype of an A. phagocytophilum mutant isolated from a sequence-defined transposon insertion library.

scholarly journals Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract

2020 ◽  
Vol 9 (23) ◽  
Author(s):  
Fabeiha Khan ◽  
Taylor Miller-Ensminger ◽  
Adelina Voukadinova ◽  
Alan J. Wolfe ◽  
Catherine Putonti
Keyword(s):  
Urinary Tract ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Vaginal Infections ◽  
Content Type ◽  
Lactobacillus Crispatus ◽  
Female Urinary Tract

ABSTRACT Lactobacillus crispatus is a Gram-positive bacterium shown to protect against urinary and vaginal infections. Here, we report the draft genome sequence of L. crispatus UMB1163, isolated from the female urinary tract.

scholarly journals Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain

2016 ◽  
Vol 82 (8) ◽  
pp. 2433-2443 ◽  
Author(s):  
Xiang Yang ◽  
Noelle R. Noyes ◽  
Enrique Doster ◽  
Jennifer N. Martin ◽  
Lyndsey M. Linke ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Shotgun Sequencing ◽  
Meat Production ◽  
Global Public Health ◽  
Beef Production ◽  
Sequencing Technology ◽  
Production Chain ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Processing Steps

ABSTRACTFoodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads forSalmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus,Clostridiumspp. (C. botulinumandC. perfringens), andCampylobacterspp. (C. jejuni,C. coli, andC. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts forS. enterica,E. coli, andC. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.

scholarly journals In VitroCulture of Previously Uncultured Oral Bacterial Phylotypes

2015 ◽  
Vol 81 (24) ◽  
pp. 8307-8314 ◽  
Author(s):  
Hayley Thompson ◽  
Alexandra Rybalka ◽  
Rebecca Moazzez ◽  
Floyd E. Dewhirst ◽  
William G. Wade
Keyword(s):  
Culture Media ◽  
Pcr Primers ◽  
Oral Bacteria ◽  
Subgingival Plaque ◽  
Community Studies ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Specific Pcr ◽  
Proteose Peptone

ABSTRACTAround a third of oral bacteria cannot be grown using conventional bacteriological culture media. Community profiling targeting 16S rRNA and shotgun metagenomics methods have proved valuable in revealing the complexity of the oral bacterial community. Studies investigating the role of oral bacteria in health and disease require phenotypic characterizations that are possible only with live cultures. The aim of this study was to develop novel culture media and use anin vitrobiofilm model to culture previously uncultured oral bacteria. Subgingival plaque samples collected from subjects with periodontitis were cultured on complex mucin-containing agar plates supplemented with proteose peptone (PPA), beef extract (BEA), or Gelysate (GA) as well as on fastidious anaerobe agar plus 5% horse blood (FAA).In vitrobiofilms inoculated with the subgingival plaque samples and proteose peptone broth (PPB) as the growth medium were established using the Calgary biofilm device. Specific PCR primers were designed and validated for the previously uncultivated oral taxaBacteroidetesbacteria HOT 365 and HOT 281,Lachnospiraceaebacteria HOT 100 and HOT 500, andClostridialesbacterium HOT 093. All agar media were able to support the growth of 10 reference strains of oral bacteria. One previously uncultivated phylotype,Actinomycessp. HOT 525, was cultivated on FAA. Of 93 previously uncultivated phylotypes found in the inocula, 26 were detected inin vitro-cultivated biofilms.Lachnospiraceaebacterium HOT 500 was successfully cultured from biofilm material harvested from PPA plates in coculture withParvimonas micraorVeillonella dispar/parvulaafter colony hybridization-directed enrichment. The establishment ofin vitrobiofilms from oral inocula enables the cultivation of previously uncultured oral bacteria and provides source material for isolation in coculture.

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