is an abundant genus of predatory soil myxobacteria, containing two species,
(for which a genome sequence is available) and
. To investigate the genomic basis of predation, we genome-sequenced 23
...strains. Genomic similarity metrics grouped the sequenced strains into at least nine distinct genomospecies, divided between two major sub-divisions of the genus, encompassing previously described diversity. The
pan-genome was found to be open, with strains exhibiting highly individual gene sets. On average, only 30.5% of each strain's gene set belonged to the core pan-genome, while more than 75% of the accessory pan-genome genes were present in less than four of the 24 genomes. The
accessory pan-proteome was enriched for the COG functional category "Secondary metabolism," with each genome containing on average 55 biosynthetic gene clusters (BGCs), of which only 20 belonged to the core pan-genome. Predatory activity was assayed against ten prey microbes and found to be mostly incongruent with phylogeny or BGC complement. Thus, predation seems multifactorial, depending partially on BGC complement, but also on the accessory pan-genome - genes most likely acquired horizontally. These observations encourage further exploration of
as a source for novel bioactive secondary metabolites and predatory proteins.
Myxobacteria are natural predators of microorganisms and the subjects of concerted efforts to identify novel antimicrobial compounds. Myxobacterial predatory activity seems to require more than just ...the possession of specific antimicrobial metabolites. Thus a holistic approach to studying predation promises novel insights into antimicrobial action. Here, we report the isolation of 113 myxobacteria from samples of soil taken from a range of habitats in mid Wales. Predatory activity of each isolate was quantified against a panel of clinically important prey organisms, including
, and three species of
. Myxobacterial isolates exhibited a wide range of predation activity profiles against the panel of prey. Efficient predation of all prey by isolates within the collection was observed, with
and
proving particularly susceptible to myxobacterial predation. Notably efficient predators tended to be proficient at predating multiple prey organisms, suggesting they possess gene(s) encoding a broad range killing activity. However, predatory activity was not congruent with phylogeny, suggesting prey range is subject to relatively rapid specialization, potentially involving lateral gene transfer. The broad but patchy prey ranges observed for natural myxobacterial isolates also implies multiple (potentially overlapping) genetic determinants are responsible for dictating predatory activity.
spp. are ubiquitous, chemoheterotrophic, filamentous gliding bacteria with the ability to prey on other microbes through a "wolf pack" mechanism. The genus currently comprises four known species (
,
...,
, and
), which produce antimicrobial secondary metabolites such as siphonazole. As part of a study isolating myxobacterial wolf pack predators, we serendipitously isolated a novel environmental strain (CA052B) from the edge of a stream at Llansteffan, United Kingdom, which was identified as a member of the
genus. A lawn culture method was utilized to analyze the predatory activity of CA052B against 10 prey organisms of clinical relevance. CA052B was found to prey on
,
,
,
,
,
,
,
, and
Purified CA052B outer membrane vesicles also exhibited killing activity against the prey organisms when tested by flow cytometry. 16S rRNA sequencing of CA052B showed 98 to 99% identity with other
species members. Comparing the genome of CA052B with the publicly available genomes of
and
revealed average nucleotide identities of only 84% and 91%, respectively, whereas the genome-to-genome distance calculation showed sequence identities of 28.2% and 46.6%, respectively. Biochemical characterization also revealed distinctions between CA052B and both
and
Thus, strain CA052B
(= DSM 107618
= NBRC 113495
) is proposed to be the type strain of a novel species,
sp. nov. The genome sequence of CA052B also revealed diverse secondary metabolite biosynthetic clusters, encouraging further exploration of its antibiotic production potential.
Predatory bacteria are able to kill and consume other microbes and are therefore of interest as potential sources of new antimicrobial substances for applications in the clinic. "Wolf pack" predators kill prey by secreting antimicrobial substances into their surroundings, and those substances can kill prey organisms independently of the predatory cells. The genus
exhibits wolf pack predation, yet its members are poorly described compared to other wolf pack predators, such as the myxobacteria. By providing a thorough characterization of a novel
species, including its predatory, biochemical, and genomic features, this study increases our understanding of genomic variation within the
genus and how that variation affects predatory activity. This will facilitate future rational exploitation of genus members (and other wolf pack predators) as sources of novel antimicrobials.
Despite widespread use in human biology, genome-wide association studies (GWAS) of bacteria are few and have, to date, focused primarily on pathogens. Myxobacteria are predatory microbes with large ...patchwork genomes, with individual strains secreting unique cocktails of predatory proteins and metabolites. We investigated whether a GWAS strategy could be applied to myxobacteria to identify genes associated with predation. Deduced proteomes from 29 myxobacterial genomes (including eight
genomes sequenced for this study), were clustered into orthologous groups, and the presence/absence of orthologues assessed in superior and inferior predators of ten prey organisms. 139 'predation genes' were identified as being associated significantly with predation, including some whose annotation suggested a testable predatory mechanism. Formaldehyde dismutase (
) was associated with superior predation of
, and predatory activity of a strain lacking
could be increased by the exogenous addition of a formaldehyde detoxifying enzyme, suggesting that production of formaldehyde by
acts as an anti-predation behaviour. This study establishes the utility of bacterial GWAS to investigate microbial processes beyond pathogenesis, giving plausible and verifiable associations between gene presence/absence and predatory phenotype. We propose that the slow growth rate of myxobacteria, coupled with their predatory mechanism of constitutive secretion, has rendered them relatively resistant to genome streamlining. The resultant genome expansion made possible their observed accumulation of prey-specific predatory genes, without requiring them to be selected for by frequent or recent predation on diverse prey, potentially explaining both the large pan-genome and broad prey range of myxobacteria.
Background and Objectives: The prevalence of child sexual abuse (CSA) in India is 18-50% depending on the population studied. To devise strategies for prevention of CSA at the primary care level, we ...studied the prevalence of CSA amongst college students aged 17-25 years. Methods: A group of medical students and their friends were sent, an anonymous questionnaire validated by experts via WhatsApp. The questionnaire assessed demography, occurrence of prior CSA and details of the sexual abuse. Results: About 574 students participated in the study. The majority of respondents were female (380, 66.2%). About 467 (81.2%) of participants were from South India. Of the 380 women and 194 men who consented to participate in the study, 218 (57.3%) and 65 (33.5%), respectively, said that they had been sexually abused in the past (p < 0.00001). The event commonly occurred at 12-14 years (22.6%), but about 53% of victims were <12 years of age. The perpetrator was usually male (93.2%), less than 30 years of age (54%) and a stranger (42.7%). The most common form of CSA from 348 instances in 283 respondents was some form of "bad touch or caresses" (56.6%). About 25.8% of those abused did not speak to anyone about the event. Only 249 respondents (43%) were counselled regarding CSA by their parents. Conclusions: The prevalence of CSA amongst South Indian college students is 49.3%. The victims were mainly girls <12 years of age and the perpetrators were mainly male (93.2%). Primary Care Physicians can play a greater role in the early detection and prevention of CSA.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
spp. are common soil-dwelling organisms which kill and consume prey microbes through the secretion of antimicrobial substances. Two species of
have been described previously (
and
). A polyphasic ...approach, including biochemical analysis of fatty acid methyl esters, substrate utilization, and sugar assimilation assays, was taken to characterize eight
species strains and the two type strains. The genomes of all strains, including that of
DSM 14696
(newly reported here), shared an average nucleotide identity below 95% and digital DNA-DNA hybridization scores of less than 70%, indicating that they belong to distinct species. In addition, we characterized the prey range and antibiotic resistance profile of each strain, illustrating the diversity of antimicrobial activity and, thus, the potential for drug discovery within the
genus. Each strain gave a distinct profile of properties, which together with their genomic differences supports the proposal of the eight candidate strains as novel species. The eight candidates are as follows:
sp. nov. (AB043A
DSM 108849
= NBRC 113887
),
sp. nov. (AB047A
DSM 108843
= NBRC 113888
),
sp. nov. (AB050A
= DSM 108846
= NBRC 114019
),
sp. nov. (CA031B
DSM 108841
= NBRC 113889
),
sp. nov. (CA040B
DSM 108850
= NBRC 113890
),
sp. nov. (CA043D
DSM 108842
= NBRC 113891
),
sp. nov. (CA051B
DSM 108844
= NBRC 114100
), and
sp. nov. (CA054A
DSM 108848
= NBRC 113892
).
is a genus of predators with broad prey ranges, whose genomes contain large numbers of gene clusters for secondary metabolite biosynthesis. The physiology and evolutionary heritage of eight
species strains were characterized using a range of analyses and assays. Multiple metrics confirmed that each strain belonged to a novel species within the
genus. The strains exhibited distinct patterns of drug resistance and predatory activity, which mirrored their possession of diverse sets of biosynthetic genes. The breadth of antimicrobial activities observed within the
genus highlights their potential for drug discovery and suggests a previous underestimation of both their taxonomic diversity and biotechnological potential. Taxonomic assignment of environmental isolates to novel species allows us to begin to characterize the diversity and evolution of members of this bacterial genus with potential biotechnological importance, guiding future bioprospecting efforts for novel biologically active metabolites and antimicrobials.
Abstract
Members of the predatory Myxococcales (myxobacteria) possess large genomes, undergo multicellular development, and produce diverse secondary metabolites, which are being actively prospected ...for novel drug discovery. To direct such efforts, it is important to understand the relationships between myxobacterial ecology, evolution, taxonomy, and genomic variation.
This study investigated the genomes and pan-genomes of organisms within the Myxococcaceae, including the genera Myxococcus and Corallococcus, the most abundant myxobacteria isolated from soils. Previously, ten species of Corallococcus were known, whereas six species of Myxococcus phylogenetically surrounded a third genus (Pyxidicoccus) composed of a single species. Here, we describe draft genome sequences of five novel species within the Myxococcaceae (Myxococcus eversor, Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis, Myxococcus vastator, Pyxidicoccus caerfyrddinensis, and Pyxidicoccus trucidator) and for the Pyxidicoccus type species strain, Pyxidicoccus fallax DSM 14698T. Genomic and physiological comparisons demonstrated clear differences between the five novel species and every other Myxococcus or Pyxidicoccus spp. type strain.
Subsequent analyses of type strain genomes showed that both the Corallococcus pan-genome and the combined Myxococcus and Pyxidicoccus (Myxococcus/Pyxidicoccus) pan-genome are large and open, but with clear differences. Genomes of Corallococcus spp. are generally smaller than those of Myxococcus/Pyxidicoccus spp. but have core genomes three times larger. Myxococcus/Pyxidicoccus spp. genomes are more variable in size, with larger and more unique sets of accessory genes than those of Corallococcus species. In both genera, biosynthetic gene clusters are relatively enriched in the shell pan-genomes, implying they grant a greater evolutionary benefit than other shell genes, presumably by conferring selective advantages during predation.
Corallococcus species are diverse in the natural environment with 10 new Corallococcus species having been characterized in just the last 5 years. As well as being an abundant myxobacterial genus, ...they produce several secondary metabolites, including Corallopyronin, Corramycin, Coralmycin, and Corallorazine. We isolated a novel strain Corallococcus spp RDP092CA from soil in South Wales, UK, using Candida albicans as prey bait and characterized its predatory activities against pathogenic bacteria and yeast.
The size of the RDP092CA genome was 8.5 Mb with a G + C content of 71.4%. Phylogenetically, RDP092CA is closely related to Corallococcus interemptor, C. coralloides, and C. exiguus. However, genome average nucleotide identity and digital DNA-DNA hybridization values are lower than 95% and 70% when compared to those type strains, implying that it belongs to a novel species. The RDP092CA genome harbours seven types of biosynthetic gene clusters (BGCs) and 152 predicted antimicrobial peptides. In predation assays, RDP092CA showed good predatory activity against Escherichia coli, Pseudomonas aeruginosa, Citrobacter freundii, and Staphylococcus aureus but not against Enterococcus faecalis. It also showed good antibiofilm activity against all five bacteria in biofilm assays. Antifungal activity against eight Candida spp. was variable, with particularly good activity against Meyerozyma guillermondii DSM 6381. Antimicrobial peptide RDP092CA_120 exhibited potent antibiofilm activity with >50% inhibition and >60% dispersion of biofilms at concentrations down to 1 μg/ml.
We propose that strain RDP092CA represents a novel species with promising antimicrobial activities, Corallococcus senghenyddensis sp. nov. (=NBRC 116490T =CCOS 2109T), based on morphological, biochemical, and genomic features.
sp.strain BUPNP1 can utilize the priority environmental pollutant 4-nitrophenol (4-NP) as its sole source of carbon and energy. In this study, genome and transcriptome sequencing were used to gain ...mechanistic insights into 4-NP degradation. The draft BUPNP1 genome is 5.56 Mbp and encodes 4,963 proteins, which are significantly enriched in hypothetical proteins compared to other
sp. A novel 4-NP catabolic 43 gene cluster "
" was identified that encodes all the genes required for the conversion of 4-NP into acetyl-CoA and succinate, via 4-nitrocatechol. The cluster also encodes pathways for the catabolism of other diverse aromatic compounds. Comparisons between BUPN1 growing on either 4-NP or glucose resulted in significant changes in the expression of many
cluster genes, and, during 4-NP growth, a loss of lipid inclusions. Moreover, fatty acid degradation/synthesis genes were found within the
cluster, suggesting fatty acids may be concurrently catabolised with 4-NP. A holistic model for the action of the
gene cluster is proposed which incorporates genetic architecture, uptake and metabolism of aromatic compounds, enzymatic activities and transcriptional regulation. The model provides testable hypotheses for further biochemical investigations into the genes of the
cluster, for potential exploitation in bioremediation.
Antimicrobial resistance (AMR) is a global concern, and as soon as new antibiotics are introduced, resistance to those agents emerges. Therefore, there is an increased appetite for alternative ...antimicrobial agents to traditional antibiotics. Here, we used in silico methods to investigate potential antimicrobial peptides (AMPs) from predatory myxobacteria. Six hundred seventy-two potential AMP sequences were extracted from eight complete myxobacterial genomes. Most putative AMPs were predicted to be active against
Klebsiella pneumoniae
with least activity being predicted against
Staphylococcus aureus
. One hundred seventeen AMPs (defined here as ‘potent putative AMPs’) were predicted to have very good activity against more than two bacterial pathogens, and these were characterized further in silico. All potent putative AMPs were predicted to have anti-inflammatory and antifungal properties, but none was predicted to be active against viruses. Twenty six (22%) of them were predicted to be hemolytic to human erythrocytes, five were predicted to have anticancer properties, and 56 (47%) were predicted to be biofilm active. In vitro assays using four synthesized AMPs showed high MIC values (e.g. So_ce_56_913 250 µg/ml and Coral_AMP411 125 µg/ml against
E. coli
). However, antibiofilm assays showed a substantial reduction in numbers (e.g. Coral_AMP411 and Myxo_mac104 showed a 69% and 73% reduction, respectively, at the lowest concentration against
E. coli
) compared to traditional antibiotics. Fourteen putative AMPs had high sequence similarity to proteins which were functionally associated with proteins of known function. The myxobacterial genomes also possessed a variety of biosynthetic gene clusters (BGCs) that can encode antimicrobial secondary metabolites, but their numbers did not correlate with those of the AMPs. We suggest that AMPs from myxobacteria are a promising source of novel antimicrobial agents with a plethora of biological properties.
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