By Charmaine Ndlela
University of the Witwatersrand (Wits) scientists have identified hundreds of potentially new microbial species in the digestive systems of wild African lions, revealing previously undocumented bacterial and viral diversity.
The reasearch, published in Animal Microbiome this week, provides the first comprehensive genome-resolved analysis of the gut microbiome of free-living African lions, opening new avenues for research into their metabolism, health and conservation.
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Researchers analysed 23 fresh faecal samples collected from 20 lions in Namibia’s Etosha National Park, reconstructing 318 bacterial genomes and 102 viral genomes from the DNA recovered.
Most of the reconstructed genomes differed substantially from those in international reference databases, suggesting they represent largely uncharacterised microbial diversity, including potentially new species.
Lead author Carl Belger, who conducted the research as part of his Master’s degree at Wits, said the lack of existing knowledge about the lion gut microbiome was a key motivation for the study.
“Very few papers had sequenced the gut microbiome of lions before,” he said. “The question was really: what does the gut microbiome of lions look like?”
A microbiome is the community of microorganisms, including bacteria and viruses, that live in a particular environment. In animals, these organisms contribute to processes such as digestion and metabolism and can provide insights into diet, environmental conditions and health.
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Although African lions have been extensively studied in terms of their behaviour, population dynamics and ecology, the microorganisms living inside their digestive systems remain comparatively poorly understood.
The Wits study tried to address this gap by using DNA sequencing and computational analysis to identify microorganisms without having to grow each organism individually in a laboratory.
The microbiome investigation formed part of wider ecological research involving lions in Etosha.
During veterinary immobilisations, researchers from different disciplines collected blood, hair and other biological samples while fitting tracking collars, enabling them to gather multiple types of information from individual animals during a single procedure.
Belger was responsible for collecting fresh faecal samples for the microbiome analysis.
“I was at the back end of the lion – at the ‘business end’, should I say,” he said.
He said the collaboration between researchers from different countries and scientific disciplines was among the most memorable aspects of the work. Teams collected different kinds of data from the same animals, reducing the need for repeated interventions.
The samples underwent extensive laboratory and computational analysis to identify and reconstruct the genetic material of the microorganisms present.
Professor Scott Hazelhurst, a senior scientist and bioinformatician at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) and co-corresponding author of the study, compared the process to completing multiple jigsaw puzzles simultaneously, with some pieces missing, damaged or duplicated.
Researchers sequenced the DNA present in each sample and used bioinformatics tools to separate genetic fragments and determine which organisms they belonged to.
“It is computationally intensive. The lion analysis involved tens of thousands of CPU hours and generated tens of terabytes of data,” Hazelhurst said.
Despite these challenges, the researchers reconstructed good-quality bacterial and viral genomes, including genetic material from organisms not previously identified at species level.
The study found that two bacterial genera, Bacteroides and Phocaeicola, accounted for 22.1% and 13.3% of the gut microbial community respectively, contrasting with findings from previous studies of captive lions.
Differences in diet, environment and geographical separation could help explain variations in microbial composition between wild and captive lions.
The findings show how genomic research can reveal microbial diversity that conventional approaches may overlook, particularly in wild animals whose microbiomes have received limited scientific attention.
The study also investigated the potential functions of the lion gut microbiome.
Researchers identified microbial pathways associated with purine metabolism. Purines are compounds found in DNA and other biological molecules and occur at high concentrations in meat and animal tissue, making their breakdown particularly relevant to carnivorous animals such as lions.
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The analysis identified nearly complete microbial metabolic pathways associated with the breakdown of the purines adenine and guanine into urea.
“Microbiota are key in any species as a key part of metabolism,” Hazelhurst said.
The researchers said further studies involving larger numbers of lions would be needed to establish how gut microbial communities differ between populations and respond to environmental conditions.
