Bergeyella porcorum sp. nov., isolated from pigs

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China

BACKGROUND

Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species.

RESULTS

In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021.

CONCLUSIONS

To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.

Characterization and whole genome sequencing of a novel strain of Bergeyella cardium related to infective endocarditis

Background

Bergeyella cardium infection is becoming increasingly prevalent in patients with infective endocarditis, suggesting its significance in disease pathogenesis. However, few studies have fully characterized this species.

Results

Herein, we report the morphological and physiological characteristics, as well as whole genome sequencing of a newly identified B. cardium HPQL strain isolated from a patient with infective endocarditis. Results from the cellular morphology and biochemical analysis provide basic knowledge on the new pathogen. The whole genome sequencing of B. cardium HPQL consists of a circular chromosome with a total length of 2,036,890 bp. No plasmid was detected. Comparative genomics were carried out then. Antibiotics resistance related genes, pathogenesis related genes, predicted insertion sequences, genome islands and predicted CRISPRs sequences were demonstrated. To our knowledge, this is the first study to provide a complete genome sequence for Bergeyella spp.

Conclusions

This study provides fundamental phenotypic and genomic information for the newly identified fastidious infective endocarditis causative bacteria, B. cardium. Our results provide insights into effective clinical diagnosis and treatment of this pathogen.

Amniculibacterium aquaticum gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a stream

Strain KYPW7^T, isolated from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain KYPW7^T were Gram-stain-negative, aerobic, non-spore forming, non-motile rods and formed white colonies. Growth occurred at 15-30 °C (optimum 25 °C), at pH 6-8 (optimum pH 6.5) and with 0-1% NaCl (optimum 0%). Phylogenetic analyses based on 16S rRNA and coding sequences of 92 protein clusters showed that strain KYPW7^T represents a novel genus in the family Flavobacteriaceae. The 16S rRNA gene sequence of strain KYPW7^T was related to the species of the genera Chryseobacterium (91.8-96.0% sequence similarity), Bergeyella (95.1-95.8%), Cloacibacterium (94.5-95.7%), Daejeonia (95.6%) and Riemerella (94.0-95.0%). Strain KYPW7^T showed less than 72% average nucleotide identity and less than 24% digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Flavobacteriaceae. The predominant fatty acids were iso-C_15:0 and iso-C_17:0 3-OH. The major isoprenoid quinone was MK-6 and the DNA G + C content was 36.8 mol%. The polar lipids had phosphatidylethanolamine, three uncharacterized aminophospholipids and an uncharacterized phospholipid. The polyamines contained homospermidine, putrescine and spermidine. On the basis of the genotypic and phenotypic data, strain KYPW7^T represents a novel species of a new genus in the family Flavobacteriaceae, for which the name Amniculibacterium aquaticum gen. nov., sp. nov. is proposed. The type strain is KYPW7^T (= BCRC 81123^T = LMG 30598^T = KCTC 62512^T).

Antimicrobial removal on piglets promotes health and higher bacterial diversity in the nasal microbiota

The view on antimicrobials has dramatically changed due to the increased knowledge on the importance of microbiota composition in different body parts. Antimicrobials can no longer be considered only beneficial, but also potentially deleterious for favourable bacterial populations. Still, the use of metaphylactic antimicrobial treatment at early stages of life is a practice in use in porcine production. Many reports have shown that antibiotics can critically affect the gut microbiota, however the effect of perinatal antimicrobial treatment on the nasal microbiota has not been explored yet. To gain insights on the potential changes in nasal microbial composition due to antimicrobial treatments, piglets from two different farms were sampled at weaning. The nasal microbiota was analysed when antimicrobial treatment was used early in life, and later, when no antimicrobial treatment was used during the lactation period. Removal of perinatal antimicrobials resulted in an increased bacterial diversity in nasal microbiota at weaning. Concurrently, elimination of antimicrobials produced an increase in the relative abundance of Prevotella and Lactobacillus, and a decrease in Moraxella and Bergeyella. These changes in microbiota composition were accompanied by an improvement of the piglets' health and a higher productivity in the nursery phase.

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets

The aim of this study was to characterise bacteria in the genus Bergeyella isolated from the nasal passages of healthy piglets. Nasal swabs from 3 to 4 week-old piglets from eight commercial domestic pig farms and one wild boar farm were cultured under aerobic conditions. Twenty-nine Bergeyella spp. isolates were identified by partial 16S rRNA gene sequencing and 11 genotypes were discriminated by enterobacterial repetitive intergenic consensus (ERIC)-PCR. Bergeyella zoohelcum and Bergeyella porcorum were identified within the 11 genotypes. Bergeyella spp. isolates exhibited resistance to serum complement and phagocytosis, poor capacity to form biofilms and were able to adhere to epithelial cells. Maneval staining was consistent with the presence of a capsule. Multiple drug resistance (resistance to three or more classes of antimicrobial agents) was present in 9/11 genotypes, including one genotype isolated from wild boar with no history of antimicrobial use. In conclusion, Bergeyella spp. isolates from the nasal cavities of piglets showed some in vitro features indicative of a potential for virulence. Further studies are necessary to identify the role of Bergeyella spp. in disease and within the nasal microbiota of pigs.

Microbiological characteristics of a novel species most closely related to 'Bergeyella cardium' as a pathogen of infectious endocarditis

Infectious endocarditis (IE) can be caused by various pathogens, from dominating agents such as viridans group streptococci and staphylococci to rare species that are less virulent and not typically considered to be pathogens. In this study, we have isolated a novel species from a patient with problem of IE which was genetically most closely related to 'Bergeyella cardium', a causative pathogen of IE first reported in Korea in 2015 as a new species of the genus Bergeyella, with a similarity of 98.8% in 16S rRNA sequences. Microbiological characteristics, including morphology, biochemical identification and antimicrobial susceptibility profiling, of this novel species were determined. This fastidious Gram-negative bacillus could only be identified successfully by molecular sequencing analysis at present, and it exhibited low minimum inhibitory concentrations to the antibiotics tested except for aminoglycosides. Phylogeny analysis revealed this novel species clustered well with 'B. cardium' and other close species of genus Bergeyella.