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Pyxidicoccus caerfyrddinensis sp. nov. Pyxidicoccus caerfyrddinensis (caer.fyrdd.in.en’sis N.L. masc. adj. caerfyrddinensis from Caerfyrddin, reflecting its isolation from soil sampled near Carmarthen [the Anglicized name for Caerfyrddin], Wales [51.86 N 4.31 W]). Vegetative cells are Gram-negative bacilli tapering slightly at the ends, measuring 0.7–0.8 m m 3.0–8.0 m m in electron micrographs. Colonies exhibit swarming motility and appear pale brown on VY-2 agar (w/v 0.5% dried baker’s yeast, 0.1% CaCl 2 2H 2 O, and 1.5% agar). Fruiting bodies are irregular spheroids, orange in color. Aerobic growth was observed at 30–40 C and at pH 6.0–9.0. Growth was unaffected by the addition of 1–3% NaCl. Hydrolyzes arginine, esculin, gelatin, p -nitrophenyl- B - D- galactopyranoside, and urea. Cells prey efficiently on Cl. nebraskensis DSM 7483, and with low efficiency upon E. coli TOP 10 and U. maydis DSM 14603. DNA GC content is 70.2 mol%. The draft genome sequence of CA032 A T is available from GenBank (accession JAAIYA01). The type strain (CA032 A T ¼ NCCB 100776 T ¼ NBBC 114353 T) was isolated from soil collected in Carmarthen, UK (gridref 51.86 N 4.31 W)., Published as part of Chambers, James, Sparks, Natalie, Sydney, Natashia, Livingstone, Paul G, Cookson, Alan R & Whitworth, David E, 2020, Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov., pp. 2289-2302 in Genome Biology and Evolution 12 (12) on page 2301, DOI: 10.1093/gbe/evaa212, http://zenodo.org/record/4561628

Myxococcus eversor sp. nov. Myxococcus eversor (e.ver’sor L. masc. n. eversor the destroyer, reflecting its destruction of prey cells). Vegetative cells are Gram-negative bacilli tapering slightly at the ends, measuring 0.6–0.7 m m 3.0–8.0 m m in electron micrographs. Colonies exhibit swarming motility and appear pale brown on VY-2 agar (w/v 0.5% dried baker’s yeast, 0.1% CaCl 2 2H 2 O, and 1.5% agar). Fruiting bodies are irregular spheroids, orange in color. Aerobic growth was observed at 30–40 C, at pH 5.0–9.0, and with the addition of 1–4% NaCl. Hydrolyzes arginine, esculin, gelatin, p -nitrophenyl- B -D-galactopyranoside, and urea. Assimilates N -acetyl-glucosamine, adipate, arabinose, caprate, citrate, gluconate, glucose, malate, maltose, mannitol, mannose, and phenyl acetate. Cells prey with low efficiency upon E. coli TOP 10, Cl. nebraskensis DSM 7483, and U. maydis DSM 14603. DNA GC content is 68.9 mol%. The draft genome sequence of AB053B T is available from GenBank (accession JAAIXY01). The type strain (AB053B T ¼ NCCB 100767 T ¼ T NBRC 114350) was isolated from soil collected from Aberystwyth University, UK (gridref 52.41 N 4.08 W)., Published as part of Chambers, James, Sparks, Natalie, Sydney, Natashia, Livingstone, Paul G, Cookson, Alan R & Whitworth, David E, 2020, Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov., pp. 2289-2302 in Genome Biology and Evolution 12 (12) on page 2300, DOI: 10.1093/gbe/evaa212, http://zenodo.org/record/4561628

Pyxidicoccus trucidator sp. nov. Pyxidicoccus trucidator (tru.ci’da.tor L. masc. n. trucidator the slaughterer, after its widespread cytotoxicity). Vegetative cells are Gram-negative bacilli tapering slightly at the ends, measuring 0.5–0.6 m m 3.0–6.0 m m in electron micrographs. Colonies exhibit swarming motility and appear pale brown on VY-2 agar (w/v 0.5% dried baker’s yeast, 0.1% CaCl 2 2H 2 O, and 1.5% agar). Fruiting bodies are irregular spheroids, orange in color. Aerobic growth was observed at 30–37 C, at pH 6.0–9.0, and in 0–1% NaCl. Hydrolyzes arginine, esculin, gelatin, p -nitrophenyl- B -D- galactopyranoside, and urea. Cells prey with low efficiency upon E. coli TOP 10, Cl. nebraskensis DSM 7483, and U. maydis DSM 14603. DNA GC content is 70.3 mol%. The draft genome sequence of CA060 A T is available from GenBank (accession JAAIXZ01). The type strain (CA060 A T ¼ NCCB 100777 T ¼ NBRC 114505 T) was isolated from soil collected in Llansteffan, UK (gridref 51.77 N 4.39 W)., Published as part of Chambers, James, Sparks, Natalie, Sydney, Natashia, Livingstone, Paul G, Cookson, Alan R & Whitworth, David E, 2020, Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov., pp. 2289-2302 in Genome Biology and Evolution 12 (12) on page 2301, DOI: 10.1093/gbe/evaa212, http://zenodo.org/record/4561628

Chambers, James, Sparks, Natalie, Sydney, Natashia, Livingstone, Paul G, Cookson, Alan R, Whitworth, David E (2020): Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov. Genome Biology and Evolution 12 (12): 2289-2302, DOI: 10.1093/gbe/evaa212, URL: http://dx.doi.org/10.1093/gbe/evaa212

Myxococcus vastator sp. nov. Myxococcus vastator (vas.ta’tor L. masc. n. vastator the ravager, after its ability to devastate colonies of prey cells). Vegetative cells are Gram-negative bacilli tapering slightly at the ends, measuring 0.6–0.7 m m 3.0–6.0 m m in electron micrographs. Colonies exhibit swarming motility and appear pale brown on VY-2 agar (w/v 0.5% dried baker’s yeast, 0.1% CaCl 2 2H 2 O, and 1.5% agar). Fruiting bodies are irregular spheroids, orange in color. Aerobic growth was observed at 30 C and at pH 8.0–9.0. Growth was unaffected by the addition of 1% NaCl. Hydrolyzes arginine and urea. Assimilates malate. Cells prey with low efficiency upon E. coli TOP 10, Cl. nebraskensis DSM 7483, and U. maydis DSM 14603. DNA GC content is 69.9 mol%. The draft genome sequence of AM301 T is available from GenBank (accession JAAIYB01). The type strain (AM301 T ¼ NCCB 100768 T ¼ NBBC 114352 T) was isolated from soil collected in the parish of Llanfairpwllgwyngyllgogerychwyrndrobwlll lantysiliogogogoch, UK (gridref 53.22 N 4.19 W).

Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov. Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis, (llan.fair.pwll.gwyn.gyll.gog.er.ych.wyrn.dro.bwllll.ant.ysil.iog.ogogoch.en’sis. N.L. masc. adj. llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogo chensis, pertaining to llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogoch, reflecting its isolation from soil collected in that parish [gridref 53.22 N 4.19 W]). Vegetative cells are Gram-negative bacilli tapering slightly at the ends, measuring 0.4–0.6 m m 4.0–7.0 m m in electron micrographs. Colonies exhibit swarming motility and appear pale brown on VY-2 agar (w/v 0.5% dried baker’s yeast, 0.1% CaCl 2 2H 2 O, and 1.5% agar). Fruiting bodies are irregular spheroids, orange in color. Aerobic growth was observed at 30 and 35 C and at pH 5.0–9.0. Growth was unaffected by the addition of 1–4% NaCl. Hydrolyzes esculin, gelatin, p -nitrophenyl- B -D- galactopyranoside, and urea. Assimilates N -acetyl-glucosamine, adipate, arabinose, glucose, malate, maltose, mannitol, mannose, and phenyl acetate. Cells prey with low efficiency upon E. coli TOP 10, Cl. nebraskensis DSM 7483, and U. maydis. DNA GC content is 68.7 mol%. The draft genome sequence of AM 401 T is available from GenBank (accession VIFM 01). The type strain (AM401 T ¼ NBRC 114351 T ¼ NBBC 100770 T) was isolated from soil collected in the parish of Llanfairpwllgwyngyllgo gerychwyrndrobwllllantysiliogogogoch, UK (gridref 53.22 N 4.19 W)., Published as part of Chambers, James, Sparks, Natalie, Sydney, Natashia, Livingstone, Paul G, Cookson, Alan R & Whitworth, David E, 2020, Comparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov., pp. 2289-2302 in Genome Biology and Evolution 12 (12) on page 2300, DOI: 10.1093/gbe/evaa212, http://zenodo.org/record/4561628

Corallococcus spp. are common soil-dwelling organisms which kill and consume prey microbes through the secretion of antimicrobial substances. Two species of Corallococcus have been described previously (Corallococcus coralloides and Corallococcus exiguus). A polyphasic approach, including biochemical analysis of fatty acid methyl esters, substrate utilization, and sugar assimilation assays, was taken to characterize eight Corallococcus species strains and the two type strains. The genomes of all strains, including that of C. exiguus DSM 14696(T) (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 Corallococcus 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: Corallococcus exercitus sp. nov. (AB043A(T) = DSM 108849(T) = NBRC 113887(T)), Corallococcus interemptor sp. nov. (AB047A(T) = DSM 108843(T) = NBRC 113888(T)), Corallococcus aberystwythensis sp. nov. (AB050A(T) = DSM 108846(T) = NBRC 114019(T)), Corallococcus praedator sp. nov. (CA031B(T) = DSM 108841(T) = NBRC 113889(T)), Corallococcus sicarius sp. nov. (CA040B(T) = DSM 108850(T) = NBRC 113890(T)), Corallococcus carmarthensis sp. nov. (CA043D(T) = DSM 108842(T) = NBRC 113891(T)), Corallococcus llansteffanensis sp. nov. (CA051B(T) = DSM 108844(T) = NBRC 114100(T)), and Corallococcus terminator sp. nov. (CA054A(T) = DSM 108848(T) = NBRC 113892(T)). IMPORTANCE Corallococcus 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 Corallococcus species strains were characterized using a range of analyses and assays. Multiple metrics confirmed that each strain belonged to a novel species within the Corallococcus 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 Corallococcus 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.

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 Klebsiella pneumoniae, Proteus mirabilis, Candida albicans, Enterococcus faecalis, and three species of Staphylococcus. 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 K. pneumoniae and C. albicans 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.

Supplementary text 1.1: Filter Sensitivity Analysis. Supplementary text 1.2: Investigating Highly Distinct Isolates. Supplementary text 1.3: Temporal Signal. Supplementary text 1.4: Hierarchical Model Selection. Supplementary text 1.5: Influence of the Priors. Table S1. Results from investigating highly distinct isolates. Table S2. Results from hierarchical model selection. (DOCX 36Â kb)