Description of ‘Arabia massiliensis’ gen. nov., sp. nov., ‘Gordonibacter massiliensis’ sp. nov., and ‘Bacilliculturomica massiliensis’ gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman

Traore, S.I.; Azhar, Esam I.; Yasir, Muhammad; Bibi, Fehmida; Fournier, Pierre‐Edouard; Jiman-Fatani, Asif A.; Delerce, Jérémy; Cadoret, F.; Lagier, Jean-Christophe; Raoult, Didier

doi:10.1016/j.nmni.2017.05.011

Cited by 7 publications

(4 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Both A. massiliensis (recently identi ed in stool material) 40 and F. nucleatum (the by far most CRCassociated bacterium in previous studies) were highly detected among the RNA sequences of the mucosa and the tumors, respectively. Compared to DNA analysis, A. massiliensis did not surpass the established cut-off, and F. nucleatum did reach it, but its relative abundance presence was low and not different between tumor and healthy mucosa specimens.…”

Section: Discussionmentioning

confidence: 74%

“…This study demonstrated how deep sequencing of both DNA and RNA enables a wider perspective of microbiome pro les: individual microbial features can vary depending on whether the metagenome or metatranscriptome is analysed. The role of the recently identi ed A. massiliensis 40 needs to be further investigated to elucidate its implications in human health. While F. nucleatum is already known to be a potential colorectal cancer biomarker for screening, diagnosis, and prognosis prediction for patient outcomes 11-14 , the association mainly with transcription of F. nucleatum may provide further insights on the role of this microorganism in CRC.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep-sequencing

Garcia‐Serrano

Mukhedkar²,

Hultin

et al. 2023

Preprint

View full text Add to dashboard Cite

Human gut microbiome studies typically focus on 16S RNA analyses and bacterial identification at the genus level. We analyzed bacterial and viral communities in colorectal tissue using both DNA and RNA sequencing and improved taxonomy resolution to species level. Specimens from 10 colorectal cancer patients and 10 matched control patients were DNA and RNA sequenced using Illumina Novaseq. Following taxonomy classification using Kraken 2, alpha and beta diversities (different metrics) as well as relative and differential abundance were calculated. There were no viral differences, but P. nesessarius had a highly increased presence in tumors (p=0.001). RNA analyses showed that A. massiliensis had a highly decreased transcription in tumors (p=0.002) while F. nucleatum transcription was highly increased in tumors (p=0.002). In conclusion, joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level identifies specific bacterial species as tumor-associated.

show abstract

Section: Discussionmentioning

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep-sequencing

Garcia‐Serrano

Mukhedkar²,

Hultin

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Previous studies on skin have detected several hundreds of human papillomavirus types when analyzing DNA sequences, but most of these viruses were not actively transcribed (apparently representing deposition). 37 Both A. massiliensis (recently identified in stool material) 38 and F. nucleatum (the by far most CRC-associated bacterium in previous studies) were highly detected among the RNA sequences of the mucosa and the tumors, respectively. Compared to DNA analysis, A. massiliensis did not surpass the established cut-off, and F. nucleatum did reach it, but its relative abundance presence was low and not different between tumor and healthy mucosa specimens.…”

Section: Discussionmentioning

confidence: 87%

“…The role of the recently identified A. massiliensis 38 and P. necessarius needs to be further investigated to elucidate their implication in human health. The present study comprised strict cut‐offs to focus the analysis only on abundant species (species present only in small amounts may conceivably represent contamination and were therefore not studied); however, validation of these “putative” findings would be desirable and findings may need to be considered carefully.…”

Section: Discussionmentioning

confidence: 99%

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue usingRNAandDNAdeep sequencing

Garcia‐Serrano,

Mukhedkar,

Hultin

et al. 2023

Cancer Medicine

View full text Add to dashboard Cite

BackgroundColorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non‐targeted deep‐sequencing strategies enable nowadays full microbiome characterization up to species level.AimWe aimed to analyze both bacterial and viral communities in CRC using these strategies.Materials & MethodsWe analyzed bacterial and viral communities using both DNA and RNA deep‐sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples.ResultsNo viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002).DiscussionSequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC.ConclusionJoint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.

show abstract

Eggerthellaceae

Gupta

2021

Bergey's Manual of Systematics of Archaea and Bacteria

View full text Add to dashboard Cite

Eg.ger.thel.la.ce'ae. N.L. fem. n. Eggerthella type genus of the family; suff. ‐ aceae ending to denote a family; Eggerthellaceae the Eggerthella family. Actinobacteria / Coriobacteriia / Eggerthellales / Eggerthellaceae The family contains the type genus Eggerthella and the following validly published genera: Adlercreutzia, Cryptobacterium, Denitrobacterium, Ellagibacter, Enteroscipio, Gordonibacter , Paraeggerthella, Parvibacter, Rubneribacter , Senegalimassilia , and Slackia . Of these genera, the genus Parvibacter, containing the species Parvibacter caecicola , was recently merged with the genus Adlercreutzia . However, evidence presented indicates that P. caecicola , which remains a validly published name, is distinct from other Adlercreutzia species and hence is retained within the genus Parvibacter . Besides the genera with validly published names, the following effectively published genera “ Arabia ,” “ Hugonella ,” “ Phoenicibacter ,” and “ Raoultibacter ” are also part of this family. The members are Gram‐positive rods or cocci and asaccharolytic except some species. Most members contain enzymes responsible for hydrolyzing amino acids such as arginine and leucine, and their growth is stimulated in the presence of arginine and some other amino acids. Most members are anaerobic, nonmotile, and do not form spores. The G + C content is in the range of 43.4–66.3% for the known species. The species of this family form a distinct clade in phylogenetic trees based on 16S rRNA gene sequences and sequences for different datasets of proteins from genomes. Additionally, the members of the family Eggerthellaceae (order Eggerthellales ) can be reliably distinguished from members of the order Coriobacteriales and other bacteria based on molecular signatures consisting of conserved indels (inserts or deletions) identified in >12 proteins described in earlier work and updated here. DNA G + C content (mol%) : 43.4–66.3 (for the known species). Type genus : Eggerthella Wade et al. 1999 VP emend. Würdemann et al. 2009.

show abstract

Description of ‘Arabia massiliensis’ gen. nov., sp. nov., ‘Gordonibacter massiliensis’ sp. nov., and ‘Bacilliculturomica massiliensis’ gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman

Cited by 7 publications

References 7 publications

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep-sequencing

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep-sequencing

Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue usingRNAandDNAdeep sequencing

Eggerthellaceae

Contact Info

Product

Resources

About