Vagococcus proximus sp. nov. and Vagococcus intermedius sp. nov., originating from modified atmosphere packaged broiler meat

During our studies on spoilage microbiomes of modified atmosphere packaged broiler meat, we isolated three strains (PNs007^T, STAA11^T and STAA25) of unknown identity. In this present polyphasic taxonomy study, including genome-based analyses, we discovered that these isolates represent two novel species belonging to the genus Vagococcus. In all phylogenetic analyses, PNs007^T was positioned very close to Vagococcus fessus but both the average nucleotide identity (ANI; 89.5 %) and digital DNA-DNA hybridization (dDDH; 38.3 %) values distinguished it as a novel vagococcal species. STAA11^T and STAA25 were genetically highly similar (16S rRNA, ANI and dDDH 100 %). The phylogenetic position of STAA11^T was adjacent to but out of the cluster containing V. fessus, Vagococcus coleopterorum and PNs007^T. According to the ANI (76.2-76.4 %) and dDDH (<22.6 %) values it also represented a novel vagococcal species. Phenotypic characteristics and chemotaxonomic properties of both novel species were typical for vagococci and they contained C_16 : 0 (25.5-30.1 %) and C_18 : 1 ω9c (67.3-73.0 %) as the major cellular fatty acids. The streptomycin-resistant genotype of STAA11^T and STAA25 allowing the growth on streptomycin thallous acetate actidione medium was considered to result from a modification in codon 104 of the rpsL gene leading to P104A substitution. The ability of STAA11^T and STAA25 to produce ammonia from arginine separated them from PNs007^T, which did not show arginine deiminase activity. We propose the names Vagococcus proximus sp. nov. (type strain PNs007^T=DSM 115185^T=CCUG 76696^T) and Vagococcus intermedius sp. nov. (type strain STAA11^T=DSM 115183^T=CCUG 76697^T) for these novel species.

Vagococcus allomyrinae sp. nov. and Enterococcus larvae sp. nov., isolated from larvae of Allomyrina dichotoma

The taxonomic positions of two novel strains isolated from larvae of an insect (Allomyrina dichotoma) collected in Jeju, Republic of Korea, were determined by a polyphasic approach. Strain BWB3-3T was closely related to the type strain of Vagococcus salmoninarum , having 97.2 % 16S rRNA gene sequence similarity, whereas strain BWM-S5T formed an independent cluster within the genus Enterococcus in the 16S rRNA gene phylogeny and the closest relative was the type strain of Enterococcus canis (98.1 % sequence similarity). The core gene analysis supported the phylogenetic positions of the isolates revealed by 16S rRNA gene phylogeny. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain BWB3-3T and the type strain of V. salmoninarum were 73.2 and 20.0 %, respectively, whereas strain BWM-S5 T showed an ANI value of 70.9 % with the type strain of Enterococcus canis . The dDDH values between strain BWM-S5T and all the type strains of Enterococcus species were ≤25.1 %. On the basis of the results obtained here, the two isolates are considered to constitute two novel species of the family Enterococcaceae , for which the names Vagococcus allomyrineae sp. nov. and Enterococcus larvae sp. nov. are proposed, with the type strains BWB3-3T (=KCTC 43277T=CCM 9080T) and BWM-S5T (=KACC 22156T=CCM 9075T), respectively.

New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus

A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17A^T and HDW17B^T, isolated from the intestine of the diving beetle Cybister lewisianus, and the dark diving beetle Hydrophilus acuminatus, respectively. Both strains were Gram-positive and facultative anaerobic cocci forming cream-colored colonies. The isolates grew optimally at 25°C, pH 7, in the presence of 0.3% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolates were members of the genus Vagococcus, and strain HDW17A^T was closely related to Vagococcus fessus CCUG 41755^T (98.9% of 16S rRNA gene sequence similarity and 74.3% of average nucleotide identity [ANI]), whereas strain HDW17B^T was closely related to Vagococcus fluvialis NCFB 2497^T (98.9% of 16S rRNA gene sequence similarity and 76.6% of ANI). Both strains contained C_16:0, and C_18:1ω9c as the major cellular fatty acids, but C_16:1ω9c was also observed only in strain HDW17B^T as the major cellular fatty acid. The respiratory quinone of the isolates was MK-7. The major polar lipid components were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The genomic DNA G + C content of strains HDW17A^T and HDW17B^T were 36.6 and 34.4%, respectively. Both strains had cell wall peptidoglycan composed of the amino acids L-alanine, glycine, D-glutamic acid, L-tryptophan, L-lysine, and L-aspartic acid, and the sugars ribose, glucose, and galactose. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW17A^T and HDW17B^T represent two novel species in the genus Vagococcus. We propose the name Vagococcus coleopterorum sp. nov. for strain HDW17A^T (= KACC 21348^T = KCTC 49324^T = JCM 33674^T) and the name Vagococcus hydrophili sp. nov. for strain HDW17B^T (= KACC 21349^T = KCTC 49325^T = JCM 33675^T).

Vagococcus zengguangii sp. nov., isolated from yak faeces

Two unknown Gram-stain-positive, catalase- and oxidasenegative, non-motile, and coccus-shaped bacteria, designated MN-17^T and MN-09, were isolated from yaks faeces (Bos grunniens) in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based comparative analyses revealed that the two strains were grouped within the genus Vagococcus, displaying the highest similarity with Vagococcus xieshaowenii CGMCC 1.16436^T (98.6%) and Vagococcus elongatus CCUG 51432^T (96.4%). Both strains grew optimally at 37°C and pH 7.0 in the presence of 0.5% (w/v) NaCl. The complete genome of MN-17^T comprises 2,085 putative genes with a total of 2,190,262 bp and an average G + C content of 36.7 mol%. The major fatty acids were C_16:0 (31.2%), C_14:0 (28.5%), and C_18:1ω9c (13.0%); the predominant respiratory quinone was MK-7 (68.8%); the peptidoglycan type was A4α(L-Lys-D-Asp); and the major polar lipid was diphosphatidylglycerol. Together, these supported the affiliation of strain MN-17^T to the genus Vagococcus. In silico DNA-DNA hybridization and the average nucleotide identity values between MN-17^T and all recognized species in the genus were 21.6-26.1% and 70.7-83.0%, respectively. MN-17^T produced acid from D-cellobiose, D-fructose, glycerol, D-glucose, N-acetyl-glucosamine, gentiobiose, D-mannose, D-maltose, D-ribose, D-saccharose, salicin, D-trehalose, and D-xylose. These results distinguished MN-17^T and MN-09 from closely related species in Vagococcus. Thus, we propose that strains MN-17^T and MN-09 represent a novel species in the genus Vagococcus, with the name Vagococcus zengguangii sp. The type strain is MN-17^T (= CGMCC 1.16726^T = GDMCC 1.1589^T = JCM 33478^T).

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49^T, was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai-Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49^T was closely related to Vagococcus elongatus CCUG 51432^T (96.5 % similarity), Vagococcus fluvialis NCFB 2497^T (96.0 %) and Vagococcus lutrae CCUG 39187^T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49^T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N-acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys-d-Asp). The major cellular fatty acids (>10 %) were C_16 : 0 (35.6 %), C_14 : 0 (17.3 %), C_18 : 1 ω9c (16.2 %) and C_16 : 1 ω9c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA-DNA hybridization of strain CF-49^T with V. fluvialis DSM 5731^T, V. elongatus CCUG 51432^Tand V. lutrae CCUG 39187^T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus, with the name Vagococcus xieshaowenii. The type strain is CF-49^T (=CGMCC 1.6436^T=GDMCC 1.1588^T=JCM 33477^T).

Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound

Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994^T was isolated from ground beef and strain SS1995^T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994^T and SS1995^T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994^T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995^T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995^T was most similar to V. penaei (99.1 %), followed by SS1994^T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994^T and SS1995^T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994^T=(CCUG 70831^T=LMG 30164^T) and Vagococcusvulneris SS1995^T=(CCUG 70832^T=LMG 30165^T) are proposed.

Fragment of the aspartyl-tRNA synthetase applicable as a shared classification and phylogenetic marker in particular representatives of the order Lactobacillales

The order Lactobacillales represents a morphologically, metabolically, and physiologically diverse group of bacteria. Lactic acid bacteria represent the core of this phylogenetic group. They are a part of epiphytic microflora, fermented dairy, meat, fruit and vegetable products, and the digestive tract of humans and animals. Despite the fact that these bacteria form a phenotypically and genotypically heterogeneous group, their phylogenetic relationship enables to propose a common genetic marker usable in classification, typing, and phylogeny. By creation of consensus sequence based on available genomic sequences of some representatives of order Lactobacillales, a specific primer-pair binding variable region of aspS gene (length of 615 nts) encoding the aspartyl-tRNA synthetase was designed. This gene has not yet been used in classification and phylogeny of the order Lactobacillales, although it meets the requirements of molecular markers (distribution and single copy in bacterial genomes, functional constancy and genetic stability, sequence variability among taxonomic units, irreplaceable role in proteosynthesis). Primers were applied on 54 type and wild Lactobacillales strains. Obtained sequences allowed to provide alignments for purpose of phylogenetic tree reconstructions that uncovered particular phylogenetic clusters of vagococci/enterococci, obligately homofermentative and heterofermentative lactobacilli. Although a relatively short fragment of the aspS gene (approximately 33% of the complete gene sequence) was evaluated, much higher sequence variability (61.8% of pairwise identity) among strains examined compared with 16S rRNA gene (90.7%, length of 1318 nt) provides a relatively simple and effective tool for classification and typing of selected representatives of the order Lactobacillales.

Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales

Detailed differentiation, classification, and phylogenetic analysis of the order Lactobacillales are performed using molecular techniques that involve the comparison of whole genomes, multilocus sequence analysis, DNA-DNA hybridisation, and 16S rRNA sequencing. Despite the wide application of the latter two techniques, issues associated with them are extensively discussed. Although complete genomic analyses are the most appropriate for phylogenetic studies, they are time-consuming and require high levels of expertise. Many phylogenetic/identification markers have been proposed for enterococci, lactobacilli, streptococci, and lactobacilli. However, none have been established for vagococci and some genera within the order Lactobacillales. The objective of the study was to find novel alternative housekeeping genes for classification, typing, and phylogenetic analysis of selected genera within the order Lactobacillales. We designed primers flanking variable regions of the infB (504 nt) and rpsB (333 nt) genes and amplified and sequenced them in 56 strains of different genera within the order Lactobacillales. Statistical analysis and characteristics of the gene regions suggested that they could be used for taxonomic purposes. Phylogenetic analyses, including assessment of (in)congruence between individual phylogenetic trees indicated the possibility of using the concatenation of the two genes as an alternative tool for the evaluation of phylogeny compared with the 16S rRNA gene representing the standard phylogenetic marker of prokaryotes. Moreover, infB, rpsB regions and their concatenate were phylogenetically consistent with two widely applied alternative genetic markers in taxonomy of particular Lactobacillales genera encoding the 60 kDa chaperonin protein (GroEL-hsp60) and phenylalanyl-tRNA synthetase, alpha subunit (pheS).

Vagococcus humatus sp. nov., isolated from soil beneath a decomposing pig carcass

A Gram-stain-positive, non-motile, coccus-shaped bacterium, designated strain C25T, was isolated from the soil beneath a decomposing pig carcass in Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain C25T belongs to the genus Vagococcus in the family Enterococcaceae of the Lactobacillales. 16S rRNA gene sequence analysis showed that strain C25T was closely related to Vagococcus lutrae CCUG 39187T (96.5 % similarity) and Enterococcus termitis LMG 8895T (95.8 %). The chemotaxonomic properties of strain C25T were consistent with those of the genus Vagococcus; the major cellular fatty acids consisted of C16 : 0, C16 : 1ω9c and C18 : 1ω9c, and the cell-wall peptidoglycan type was based on meso-diaminopimelic acid. The G+C content of the genomic DNA was 44 mol%. On the basis of phylogenetic inference, fatty acid profile, and chemotaxonomic and other phenotypic properties, strain C25T is clearly differentiated from closely related type strains of the genus Vagococcus and represents a novel species in this genus, for which the name Vagococcus humatus sp. nov. is proposed. The type strain is C25T (=KEMB 562-002T=JCM 31581T).

Complete and Assembled Genome Sequence of Vagococcus teuberi DSM 21459T, a Novel Species Isolated from Fermented Cow Milk in Mali

The genome of Vagococcus teuberi DSM 21459^T, a strain isolated from Malian fermented milk, was sequenced using single-molecule real-time sequencing. The genome of V. teuberi DSM 21459^T is the first sequenced genome of this novel species and the second genome among the genus Vagococcus.

Lactobacillus vespulae sp. nov., isolated from gut of a queen wasp (Vespula vulgaris)

A Gram-stain-positive, oxidase- and catalase-negative, rod-shaped, facultatively anaerobic bacterial strain, DCY75T, was isolated from a queen wasp (Vespula vulgaris). Growth occurred at 4–37 °C (optimum, 30 °C), at pH 3.5–8.0 (optimum, pH 5.0–6.0) and with ≤ 7.0 % (w/v) NaCl. Strain DCY75T produced gas during growth on glucose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DCY75T belonged to the genus Lactobacillus and was closely related to Lactobacillus sanfranciscensis ATCC 27651T and Lactobacillus lindneri DSM 20690T at sequence similarities of 96.7 and 96.4 %, respectively. A comparison of two housekeeping genes, pheS and rpoA, revealed that strain DCT75T was well separated from other species of the genus Lactobacillus. Strain DCY75T produced d- and l-lactic acid isomers in a ratio of 22.5 : 77.5 (v/v). The major fatty acids were summed feature 8 (comprising C18 :  1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω9c and C18 : 0.The peptidoglycan structure was of the A4α (l-Lys–d-Asp) type. Cell-wall sugars were glucose, galactose and ribose. The DNA G+C content was 35.5 ± 1.3 mol%. Based on phenotypic and genotypic properties, strain DCY75T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus vespulae sp. nov. is proposed. The type strain is DCY75T ( = KCTC 21023T = JCM 19742T).

Rearing and foraging affects bumblebee (Bombus terrestris) gut microbiota

Bumblebees are ecologically and economically important as pollinators of crop and wild plants, especially in temperate systems. Species, such as the buff-tailed bumblebee (Bombus terrestris), are reared commercially to pollinate high-value crops. Their highly specific gut microbiota, characterized by low diversity, may affect nutrition and immunity and are likely to be important for fitness and colony health. However, little is known about how environmental factors affect bacterial community structure. We analysed the gut microbiota from three groups of worker bumblebees (B. terrestris) from distinct colonies that varied in rearing and foraging characteristics: commercially reared with restricted foraging (RR); commercially reared with outside foraging (RF); and wild-caught workers (W). Contrary to previous studies, which indicate that bacterial communities are highly conserved across workers, we found that RF individuals had an intermediate community structure compared with RR and W types. Further, this was shaped by differences in the abundances of common operational taxonomic units (OTUs) and the diversity of rare OTUs present, which we propose results from an increase in the variety of carbohydrates obtained through foraging.