Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as ‘shared’ OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

• Publication year

  2013

• Venue

  PLoS ONE

• Publication date

  2013-04-23

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pone.0061463PMID 23626688PMCID 3634081
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Putative reductive acetogens and fibrolytic bacteria were also detected in the foregut samples.

  Confidence 0.89

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• Eleven dominant OTUs separated the three host species, and the classified taxa included unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp., and Syntrophococcus sucromutans.

  Confidence 0.90

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• The foregut bacterial communities differed significantly among Macropus rufus, Macropus giganteus, and Macropus robustus, enabling host-species differentiation.

  Confidence 0.95

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• Thirty-two shared OTUs occurred in every sample, and they belonged to Firmicutes or Bacteroidetes.

  Confidence 0.97

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• Filtering the V3/V4 16S rRNA pyrosequencing data yielded 5,040 OTUs from the macropod foregut samples.

  Confidence 0.98

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review

• 454-amplicon pyrosequencing

  method

  A sequencing approach used to profile amplified 16S rRNA gene fragments in the foregut samples.

  Aliases: pyrosequencing, 454 sequencing

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• alpha and beta diversity measures

  measurements

  Community diversity metrics used to compare microbial variation within and between samples.

  Aliases: alpha diversity, beta diversity

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• bacteroidetes

  taxon

  A bacterial phylum represented among the OTU classifications discussed for the foregut communities.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• dominant otus

  taxonomic unit

  The subset of OTUs highlighted as the main contributors to differences among host species.

  Aliases: eleven dominant OTUs

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• fibrolytic bacteria

  taxon

  Bacteria associated with fiber degradation that were considered putative members of the foregut community.

  Aliases: fibrolytics

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• firmicutes

  taxon

  A bacterial phylum represented among the OTU classifications discussed for the foregut communities.

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• host species differentiation

  observation

  Separation of the sampled macropod hosts by their foregut bacterial community profiles.

  Aliases: species differentiation

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• macropod foregut bacterial community

  community

  The bacterial community sampled from the foregut of Queensland macropods in this survey.

  Aliases: foregut microbiome, foregut bacterial community

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• prevotella spp.

  taxon

  Bacteria assigned to the genus Prevotella.

  Aliases: Prevotella

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• reductive acetogens

  taxon

  Acetogenic bacteria capable of reductive carbon dioxide fixation discussed as putative members of the foregut community.

  Aliases: acetogens

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• shared otus

  taxonomic unit

  Operational taxonomic units reported as present in every sampled foregut community.

  Aliases: shared operational taxonomic units

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• syntrophococcus sucromutans

  taxon

  A bacterial species name used for one of the classified dominant OTUs.

  Aliases: S. sucromutans

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• unclassified bacteroidales

  taxon

  An unclassified bacterial lineage assigned to the Bacteroidales order.

  Aliases: Bacteroidales

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• unclassified ruminococcaceae

  taxon

  An unclassified bacterial lineage assigned to the Ruminococcaceae family.

  Aliases: Ruminococcaceae

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review
• v3/v4 region of 16s rrna gene

  genetic region

  The 16S rRNA gene amplicon region targeted for microbial community profiling in the survey.

  Aliases: V3/V4, V3 V4 region

  박진우 (dztg5apj7m) extractionB (s683577b42) reviewq (76h6bfydm6) review

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