Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries

K. Tajima, Rustam Aminov, T. Nagamine, K. Ogata, M. Nakamura, H. Matsui, Y. Benno

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Abstract

Molecular diversity of rumen bacteria was analyzed by PCR amplification and sequencing of 16S rDNA clone libraries prepared from the rumen content of Holstein cows fasted for 16 h. A total of 84 clones, containing almost full size 16S rDNA sequences (about 1.5 kb long), were completely sequenced and subjected to an on line similarity search. Four sequences from the 84 clones closely resembled that of Butyrivibro fibrisolvens and one clone was found to be related to Treponema bryantii. For 38% of the sequences, the similarity with database sequences was in the range of 90%-98% and for the remaining 56% the similarity was less than 90%. The bacterial community structure was also revealed by phylogenetic placement of sequences in relation to different fractions of rumen content. In the library from the rumen fluid, the sequences were affiliated with the following major phyla: low G+C Gram-positive bacteria (52.4%), Cytophaga-Flexibacter-Bacteroides (38.1%), Proteobacteria (4.7%) and Spirochaetes (2.4%). 2.4% had an uncertain affiliation. The vast majority of sequences from the rumen solids were found to be related to law G+C Gram-positive bacteria (71.4%) and the remaining sequences were placed within the Cytophaga-Flexibacter-Bacteroides (26.2%) and Spirochaetes (2.4%) phyla. (C) 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
Original languageEnglish
JournalF E M S Microbiology Ecology
Volume29
Issue number2
Pages (from-to)159-169
Number of pages11
ISSN0168-6496
DOIs
Publication statusPublished - 1999
Externally publishedYes

Keywords

  • ribosome DNA
  • article
  • Bacteroides
  • cow
  • DNA sequence
  • Flexibacteraceae
  • Gram positive bacterium
  • nonhuman
  • nucleotide sequence
  • polymerase chain reaction
  • priority journal
  • rumen microorganism
  • sequence homology
  • spirochete
  • Treponema
  • Bacteria (microorganisms)
  • Butyrivibrio fibrisolvens
  • Cytophaga
  • Firmicutes
  • Flexibacter
  • Posibacteria
  • Prokaryota
  • Proteobacteria
  • Spirochaetales
  • Spirochaetes
  • Treponema bryanti
  • Treponema bryantii
  • 16S rDNA library
  • Bacterial diversity
  • Phylogenetic analysis
  • Rumen contents
  • MICROBIOLOGY
  • RIBOSOMAL-RNA GENES
  • PHYLOGENETIC ANALYSIS
  • SP-NOV
  • BACTEROIDES
  • PREVOTELLA
  • PROPOSAL
  • CLOSTRIDIUM
  • RUMINICOLA
  • ALIGNMENT
  • STRAINS
  • rumen contents
  • 168 rDNA library
  • bacterial diversity
  • phylogenetic analysis
  • rumen bacterial diversity
  • Actinomycetes and Related Organisms Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Irregular Nonsporing Gram-Positive Rods [08890] Butyrivibrio fibrisolvens
  • Anaerobic Gram-Negative Rods Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteroidaceae [06901] Bacteroides
  • Cytophagales Nonfruiting Gliding Bacteria Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Cytophagaceae [08511] Cytophaga
  • Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteria [05000] Proteobacteria sp. Spirochaetes
  • Nonfruiting Gliding Bacteria Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Cytophagales [08510] Flexibacter
  • Spirochaetales Spirochetes Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Spirochaetaceae [06112] Treponema bryantii
  • bacteria 16S rDNA gene
  • 14001, Digestive system - General and methods
  • 30000, Bacteriology, general and systematic
  • Ingestion and Assimilation
  • Digestive System
  • Population Studies

Cite this

Tajima, K., Aminov, R., Nagamine, T., Ogata, K., Nakamura, M., Matsui, H., & Benno, Y. (1999). Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. F E M S Microbiology Ecology, 29(2), 159-169. https://doi.org/10.1016/S0168-6496(99)00008-2