Comparing different computational approaches for detecting long-term vertical transmission in host-associated...

Area of Science:

• Microbiology
• Evolutionary Biology
• Bioinformatics

Background:

• Long-term vertical transmission of gut bacteria is considered frequent and functionally significant in mammals.
• Phylogenetic methods are used to identify vertically transmitted bacteria within species-rich microbiota during host evolution.
• Previous applications of these methods to mammal microbiota have yielded conflicting results, and their performance with slowly evolving markers is unclear.

Purpose of the Study:

• To statistically evaluate the performance of widely-used phylogenetic approaches for detecting vertical bacterial transmission.
• To compare the strengths and weaknesses of global-fit (ParaFit, PACo) and event-based (ALE, HOME) methods.
• To assess the extent of vertical gut bacterial transmission in primates.

Main Methods:

• Simulations were used to test the statistical performance of ParaFit, PACo, ALE, and HOME phylogenetic approaches.
• The impact of bacterial DNA sequence variation on method performance was investigated.
• The methods were applied to analyze the gut microbiota composition of primates.

Main Results:

• Phylogenetic methods exhibit complementary strengths and weaknesses influenced by bacterial DNA sequence variation.
• ALE performed better with high sequence variation, while HOME was more effective with low variation.
• Global-fit methods (ParaFit, PACo) showed higher false positive rates but were computationally faster.
• Analysis of primate gut microbiota suggested limited vertical transmission of bacteria.

Conclusions:

• No single phylogenetic method is universally superior for detecting vertical bacterial transmission; methods are complementary.
• The choice of method should consider the level of bacterial DNA sequence variation.
• Vertical transmission appears to account for only a small fraction of the gut bacteria found in primates.