We've just published a new paper in Microbial Biotechnology with our collaborators in AgResearch Dr. Sinead Leahy, Dr. Bill Kelly and Dr. Gemma Henderson. This was part of the Hungate 1000 project, which has the aim of producing a reference set of rumen microbial genome sequences. The paper investigates the extent of the culturing effort of bacteria from the rumen so far, compared to the diversity predicted from combining all available 16S surveys (see figure).
Interestingly, Some of the most abundant clades of bacteria from the rumen (highlighted in red) have some of the fewest cultured representatives, highlighting the challenge to be overcome by the Hungate project.
For instance, 535 cultured RDP isolates mapped to only 107 of the 2,406 rumen OTUs in the attached tree, meaning the same OTU has been isolated many times. Additionally, only 6 OTUs from the most abundant clade (Clade I, which contained 286 OTUs and made up 20% of all the sequence from the studies analysed) had representatives isolated (in the RDP database). We have made the tree available for interactive exploration on iTOL here.
This information is being used to direct the sequencing efforts to ensure a representative sampling is achieved. The paper is open access and available here.
For instance, 535 cultured RDP isolates mapped to only 107 of the 2,406 rumen OTUs in the attached tree, meaning the same OTU has been isolated many times. Additionally, only 6 OTUs from the most abundant clade (Clade I, which contained 286 OTUs and made up 20% of all the sequence from the studies analysed) had representatives isolated (in the RDP database). We have made the tree available for interactive exploration on iTOL here.
This information is being used to direct the sequencing efforts to ensure a representative sampling is achieved. The paper is open access and available here.