Pseudoscardovia suis gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of wild pigs (Sus scrofa)

Killer, Jiří; Mrázek, Jakub; Bunešová, Věra; Havlík, J.; Koppová, I.; Benada, Oldřich; Rada, V.; Kopečný, J.; Vlková, Eva

doi:10.1016/j.syapm.2012.09.001

Cited by 35 publications

(12 citation statements)

References 26 publications

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“…However, genome sequence information for members of several newly described Scardovia -related genera (viz. Aeriscardovia, Neoscardovia , and Pseudoscardovia ), is lacking at present (Simpson et al, 2004 ; García-Aljaro et al, 2012 ; Killer et al, 2013 ). In future studies, depending upon whether the species from these genera branch with the Scardovia -clade and their sharing of the molecular signatures specific for this clade, the possibility of dividing the order Bifidobacteriales into two or more families could be considered.…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, Gardnerella vaginalis is indicated to play an important role in the pathogenesis of bacterial vaginosis and urinary tract infections (Smith et al, 1992 ; Bradshaw et al, 2006 ; Alves et al, 2014 ; Kenyon and Osbak, 2014 ). The order Bifidobacteriales is part of the phylum Actinobacteria (Ventura et al, 2007b ; Zhi et al, 2009 ; Gao and Gupta, 2012 ) and it harbors a single family, Bifidobacteriaceae , containing >50 recognized species (Biavati, 2012 ; Lugli et al, 2014 ; Milani et al, 2014 ; Parte, 2014 ) that are grouped into eight genera: Aeriscardovia, Alloscardovia, Bifidobacterium, Gardnerella, Pseudoscardovia, Neoscardovia, Parascardovia , and Scardovia (Jian and Dong, 2002 ; Simpson et al, 2004 ; Huys et al, 2007 ; Biavati and Mattarelli, 2012 ; García-Aljaro et al, 2012 ; Storms and Vandamme, 2012 ; Killer et al, 2013 ). Of these, the genus Bifidobacterium , encompassing 39 species and 9 subspecies, forms the largest group and accounts for more than 75% of the described taxa within the order Bifidobacteriales (Biavati and Mattarelli, 2012 ; Milani et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades

et al. 2016

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The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these bacteria. The Bifidobacteriales-specific CSIs, found in important proteins, are predicted to play important roles in modifying the cellular functions of the affected proteins. Hence, biochemical studies on the cellular functions of these CSIs could lead to discovery of novel characteristics of either all Bifidobacteriales, or specific groups of bacteria within this order. Some of the functions affected/modified by these genetic changes could also be important for the probiotic/pathogenic activities of the bifidobacteria.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades

et al. 2016

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“… Strains are in relation to newly described Lactobacillus species isolated from the digestive tract of honey bees ( Apis mellifera ) and bumblebees ( Bombus terrestris ) [ 23 , 24 , 45 ]. The tree was reconstructed using the maximum-likelihood method based on 16S rRNA (length of 1350 nt) as described previously [ 46 ]. Bootstrap values, expressed as percentages of 1000 datasets, are shown at nodes.…”

Section: Supporting Informationmentioning

confidence: 99%

“… They represent 2 species of recently described new genera within newly established family Orbaceae. Tree was reconstructed using the maximum-likelihood method based on 16S rRNA (length of 1309 nt), as described previously [ 46 ]. Bootstrap values, expressed as percentages of 1000 datasets, are shown at nodes.…”

Section: Supporting Informationmentioning

confidence: 99%

Variation in Honey Bee Gut Microbial Diversity Affected by Ontogenetic Stage, Age and Geographic Location

et al. 2015

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Social honey bees, Apis mellifera, host a set of distinct microbiota, which is similar across the continents and various honey bee species. Some of these bacteria, such as lactobacilli, have been linked to immunity and defence against pathogens. Pathogen defence is crucial, particularly in larval stages, as many pathogens affect the brood. However, information on larval microbiota is conflicting.Seven developmental stages and drones were sampled from 3 colonies at each of the 4 geographic locations of A. mellifera carnica, and the samples were maintained separately for analysis. We analysed the variation and abundance of important bacterial groups and taxa in the collected bees.Major bacterial groups were evaluated over the entire life of honey bee individuals, where digestive tracts of same aged bees were sampled in the course of time. The results showed that the microbial tract of 6-day-old 5th instar larvae were nearly equally rich in total microbial counts per total digestive tract weight as foraging bees, showing a high percentage of various lactobacilli (Firmicutes) and Gilliamella apicola (Gammaproteobacteria 1). However, during pupation, microbial counts were significantly reduced but recovered quickly by 6 days post-emergence. Between emergence and day 6, imago reached the highest counts of Firmicutes and Gammaproteobacteria, which then gradually declined with bee age. Redundancy analysis conducted using denaturing gradient gel electrophoresis identified bacterial species that were characteristic of each developmental stage.The results suggest that 3-day 4th instar larvae contain low microbial counts that increase 2-fold by day 6 and then decrease during pupation. Microbial succession of the imago begins soon after emergence. We found that bacterial counts do not show only yearly cycles within a colony, but vary on the individual level. Sampling and pooling adult bees or 6th day larvae may lead to high errors and variability, as both of these stages may be undergoing dynamic succession.

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“…Scardovial genera were separated from bifidobacteria within the family Bifidobacteriaceae (Stackebrandt et al , 1997) on the basis of phylogenetic, genotypic and phenotypic analyses (Jian & Dong, 2002; Simpson et al , 2004; Killer et al , 2010a; García-Aljaro et al , 2012). Representatives of scardovial genera ( Aeriscardovia , Alloscardovia , ‘ Neoscardovia ’, Parascardovia , ‘ Pseudoscardovia ’ and Scardovia ) were found in the porcine caecum, porcine slurries, digestive tract of wild pigs (Killer et al , 2013), human dental caries (Crociani et al , 1996) and human clinical samples (Huys et al , 2007). Recently, a new genus, ‘ Bombiscardovia ’, of the family Bifidobacteriaceae was isolated from the digestive tract of bumblebees (Killer et al , 2010a).…”

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confidence: 99%

Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov.

Killer

Ročková

Vlková

et al. 2013

International Journal of Systematic and Evolutionary Microbiology

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Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov. Scardovial genera were separated from bifidobacteria within the family Bifidobacteriaceae (Stackebrandt et al., 1997) on the basis of phylogenetic, genotypic and phenotypic analyses (Jian & Dong, 2002;Simpson et al., 2004;Killer et al., 2010a; García-Aljaro et al., 2012). Representatives of scardovial genera (Aeriscardovia, Alloscardovia, 'Neoscardovia', Parascardovia, 'Pseudoscardovia' and Scardovia) were found in the porcine caecum, porcine slurries, digestive tract of wild pigs (Killer et al., 2013), human dental caries (Crociani et al., 1996) and Abbreviation: F6PPK, fructose-6-phosphate phosphoketolase.The GenBank/EMBL/DDBJ accession numbers for the partial 16S rRNA gene, hsp60, Xfp and fusA sequences of strain M8 T are JQ363617, JQ363647, JQ363675 and JQ363637, respectively. GenBank/EMBL/DDBJ accession numbers for some of these phylogenetic markers obtained within this study for type strains of A. omnicolens and A. criceti comb. nov. are shown in the phylogenetic trees.Four supplementary figures and three supplementary tables are available with the online version of this paper.

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Pseudoscardovia suis gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of wild pigs (Sus scrofa)

Cited by 35 publications

References 26 publications

Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades

Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades

Variation in Honey Bee Gut Microbial Diversity Affected by Ontogenetic Stage, Age and Geographic Location

Alloscardovia macacae sp. nov., isolated from the milk of a macaque (Macaca mulatta), emended description of the genus Alloscardovia and proposal of Alloscardovia criceti comb. nov.

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