期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2016
卷号：113
期号：48
页码：13887-13892
DOI：10.1073/pnas.1610856113
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceMany bacteria are adapted to live in specific locations in animal hosts, even while these same locations exclude colonization by most microorganisms. However, the genetic underpinnings enabling successful colonization are largely unclear. We developed a system to genetically manipulate Snodgrassella alvi, a bacterium restricted to bees, and explored the factors permitting S. alvi to establish within its natural habitat in the bee digestive tract. Using high-throughput methods that screen the entire genome, we find that host colonization is dependent on genes mediating cell surface interactions (e.g., adhesion), metabolism under nutrient limitation, and responses to various stresses. This study demonstrates the genetic tractability of the bee gut microbiota, an emerging system with parallels to the human microbiome. Animal guts are often colonized by host-specialized bacterial species to the exclusion of other transient microorganisms, but the genetic basis of colonization ability is largely unknown. The bacterium Snodgrassella alvi is a dominant gut symbiont in honey bees, specialized in colonizing the hindgut epithelium. We developed methods for transposon-based mutagenesis in S. alvi and, using high-throughput DNA sequencing, screened genome-wide transposon insertion (Tn-seq) and transcriptome (RNA-seq) libraries to characterize both the essential genome and the genes facilitating host colonization. Comparison of Tn-seq results from laboratory cultures and from monoinoculated worker bees reveal that 519 of 2,226 protein-coding genes in S. alvi are essential in culture, whereas 399 are not essential but are beneficial for gut colonization. Genes facilitating colonization fall into three broad functional categories: extracellular interactions, metabolism, and stress responses. Extracellular components with strong fitness benefits in vivo include trimeric autotransporter adhesins, O antigens, and type IV pili (T4P). Experiments with T4P mutants establish that T4P in S. alvi likely function in attachment and biofilm formation, with knockouts experiencing a competitive disadvantage in vivo. Metabolic processes promoting colonization include essential amino acid biosynthesis and iron acquisition pathways, implying nutrient scarcity within the hindgut environment. Mechanisms to deal with various stressors, such as for the repair of double-stranded DNA breaks and protein quality control, are also critical in vivo. This genome-wide study identifies numerous genetic networks underlying colonization by a gut commensal in its native host environment, including some known from more targeted studies in other host-microbe symbioses.
