Isolation of Cellulolytic Bacteria, and Metagenomic Characterisation of Fibre-Rich Human Guts

  • Omololu Fagunwa

Student thesis: Doctoral Thesis


The last few decades have seen a rise in demand for cellulosic bio commodities as alternatives to fossil-based commodities. Lignocellulosic biomass is one of the most abundant, cheap, and renewable feedstocks used due to its rich cellulose content. Unfortunately, the recalcitrant nature of lignocellulose hinders achieving efficient and cost-effective production of these commodities. Hence, there is a growing industrial need of enzymes that will depolymerise lignocellulose to accessible substrates. Since a typical vegetarian diet contains plants with lignified cell walls, examining the gut microbiota and microbiome of people on high fibre may help elucidate lignocellulose degradation, and perhaps reveal novel enzymes.

Therefore, this research aimed to isolate cellulose-degrading bacteria and characterise the gut microbiota of individuals on different diet types using culture-dependent and culture-independent methods. The result indicated that culture dependent methods using existing and newly formulated cellulose-based media supported the isolation of bacteria such as Blautia luti, Collinsella aeroficiens, Pediococcus acidilacti and six species of Lactobacillus. Likewise, more probiotics and cellulose-degrading bacteria were isolated from the gut of individuals on vegetarian diets compared to those on ‘westernised’ diets. Carbohydrate structure analyses showed that the Lactobacillus mucosae VG1 strain isolated from this work produced novel D-galactan, branched hexassacharides repeating unit exopolysaccharides. This is the first EPS from L. mucosae strain to have a fully characterised chemical structure.

Metagenome analyses from this study revealed that irrespective of diet type, the dominant phyla in the human gut are Firmicutes, followed by Bacteroidetes, Actinobacteria, Proteobacteria and Verrucomicrobia. However, amplicon sequence and metagenomic analyses indicated that it may be challenging to see distinct Firmicutes/Bacteroidetes ratio based on fibre consumption, suggesting the need to explore other dietary compositions (e.g. salt intake). Low dietary salt intake relates to higher abundance and diversity of complex polysaccharide-degrading bacteria and probiotics. This also provided a microbiological explanation for the nutritional guidance that advises ≤5,000mg/day dietary salt intake in humans.

Reconstructed microbial pathways indicated that taxa within the Bacteroides genus, produced 25% of the longevity enzymes detected; were not involved in the hyperglycaemia pathway; and had rich abundance and diversity in pro-health classification viz vegetarian, low salt, and high fibre guts. However, Prevotella copri was a significant cellulose degrader, though it may not ensure complete degradation on its own. In short, for complete hydrolysis of cellulose, consortium of cellulases from various bacteria is proposed for future work. The first initial degradation of cellulose to cellobiose may require a microbial consortium comprising Prevotella copri, Bacteroides (especially B. uniformis and B. cellulosilyticus), and Lachnospiraceae. Then a second consortium that ensures complete degradation to glucose may include Faecalibacterium prausnitzii, Clostridium spp., Ruminococcus, Holdemanella biformis, Coprobacillus, Lachnospiraceae and Eubacterium. This study had expanded the current knowledge on lignocellulose degradation and had revealed the bacteria involved in each catalytic processes in the gut of people on high fibre diets. Future works may consider investigating the ability of these bacteria to degrade various lignocellulosic materials.
Date of Award6 Sep 2022
Original languageEnglish
SupervisorPaul Humphreys (Main Supervisor)

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