Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken

Saputra, Sugiyono; Irisawa, Tomohiro; Sakamoto, Mitsuo; Kitahara, Maki; Sulistiani, Sulistiani Sulistiani; Yulinery, Titin; Ohkuma, Moriya; Dinoto, Achmad

doi:10.1099/ijsem.0.000573

Cited by 16 publications

(8 citation statements)

References 25 publications

(27 reference statements)

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“…Furthermore, Bacteroides was enriched significantly in the BL medium, which indicated that it could be isolated in the BL medium. This result is consistent with other studies, and some novel Bacteroides species were isolated using medium containing blood (Bakir et al 2006a , b ; Kitahara et al 2012 ; Saputra et al 2015 ). Interestingly, 692 unique anaerobic episodes were isolated from the blood cultures in a clinical study, while the Bacteroides spp.…”

Section: Discussionsupporting

confidence: 92%

Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure

Yan

et al. 2021

AMB Expr

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Isolating relevant microorganisms is still a substantial challenge that limits the use of bacteria in the maintenance of human health. To confirm which media and which bacterial colony densities can enrich certain kinds of bacteria, we selected eight common media and used them to enrich the gut microorganisms on agar plates. Then, we calculated the numbers of bacterial colonies and collected the bacterial culture mixtures from each kind of medium. Using the Illumina HiSeq platform, we analyzed the composition and diversity of the culture-enriched gut bacterial community. Our data suggested that medium supplemented with blood could increase the diversity of the bacterial community. In addition, beef powder and peptone could significantly change the culture-enriched bacterial community. A moderate density (100–150 colony-forming units per plate) was optimal for obtaining the highest diversity on the agar. Similarly, membrane transport was significantly enriched in the moderate-density group, which indicated a more active metabolism in this density range. Overall, these results reveal the optimal culture conditions, including the densities of colonies and nutritional components for various gut bacteria, that provide a novel strategy for isolating bacteria in a way that is targeted and avoids blinded and repetitive work.

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Section: Discussionsupporting

confidence: 92%

Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure

Yan

et al. 2021

AMB Expr

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“…The description is as for Bacteroides caecigallinarum (Saputra et al, 2015). The type strain is C13EG111 = InaCC B455 = NBRC 110959.…”

Section: Discussionmentioning

confidence: 99%

“…Many Bacteroidetes produce pigments, particularly carotenoids (Goodwin, 1980; Sowmya and Sachindra, 2016) and flexirubin-like pigments (Reichenbach et al, 1974, 1980); in some cases proteorhodopsin has been observed (González et al, 2008; Yoshizawa et al, 2012). The cell shape ranges from short rods to long filaments (Saputra et al, 2015; Hahnke R. L. et al, 2016); longer cells are often flexible, including curved or helical shapes (Eder et al, 2015; Shakeela et al, 2015a). Spherical degenerative forms called “spheroblasts” are known from Flavobacterium (Bernardet and Bowman, 2006).…”

Section: Introductionmentioning

confidence: 99%

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

et al. 2019

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Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

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“…B. dorei , B. clarus , B. uniformis , B. xylanisolvens , B. ovatus , B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. salanitronis , B. caecigallinarum , M. massiliensis , B. plebeius , B. coprocola , B. caecicola and B. mediterraneensis were specific for chickens. A certain degree of host adaptation could be expected as B. dorei , B. uniformis , B. xylanisolvens and B. ovatus were reported as common to human gut microbiota [ 8 , 9 , 25 , 26 ] and B. plebeius and B. caecigallinarum are common in chickens [ 27 , 28 ]. However, the extent and contrast of the host adaptation was unexpected, since representatives of 12 species were originally isolated from chickens [ 7 ] and B. thetaiotaomicron and B. vulgatus were originally cultured from pig faeces.…”

Section: Discussionmentioning

confidence: 99%

Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

et al. 2020

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Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.

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Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken

Cited by 16 publications

References 25 publications

Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure

Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

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