Highly multiplexed spatial mapping of microbial communities

Abstract

Mapping the complex biogeography of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge because of the high density 1 and rich diversity 2 of species in environmental microbiomes and the limitations of optical imaging technology 3 – 6 . Here, we introduce High Phylogenetic Resolution microbiome mapping by Fluorescence in situ Hybridization (HiPR-FISH), a versatile technology that uses binary encoding, spectral imaging, and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrate the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli isolates, each fluorescently labeled with a unique binary barcode. HiPR-FISH, in conjunction with custom algorithms for automated probe design and single-cell image analysis, reveals the disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment and the longitudinal stability of spatial architectures in the human oral plaque microbiome. Combined with super-resolution imaging, HiPR-FISH reveals the diverse ribosome organization strategies of human oral microbial taxa. HiPR-FISH provides a framework for analyzing the spatial ecology of environmental microbial communities at single-cell resolution.

Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR

“…As we have shown here, OIL-PCR can detect direct physical associations of bacteria. Such interactions are important for understanding biofilm composition 28 , identifying endosymbionts, or detecting cross-feeding bacteria which require the direct exchange of nutrients to grow 29,30 , information which could allow for culturing of these often unculturable species. Further, targeting functional metabolic genes detected in metagenomes, but present at low abundance in bacterial communities, could identify novel bacteria involved in nutrient cycling which has remained a persistent challenge in the field of bacterial ecology 31 .…”

Gut Microbiome and Drug Metabolism

“…Кроме того, сочетание метаболитов нескольких бактерий может приводить к иным вариантам биотрансформации по сравнению с биотрансформацией метаболитами этих же бактерий по отдельности. Для изучения неоднородности распределения отдельных видов бактерий может быть применена, например, технология HiPR-FISH, позволяющая идентифицировать и в высоком разрешении картировать пространственное распределение микроорганизмов в сложном сообществе [13].…”

“…Данные многочисленных метагеномных исследований свидетельствуют, что количество эукариотических и бактериальных клеток в организме человека сопоставимооколо 3.0х10 13 [2]; при этом количество генов в метагеноме кишечника человека составляет около 530000 против 30000 в геноме человека [3]. Согласно теории функциональной избыточности [4], кишечная экосистема образована «бактериальным супервидом» с очень большим геномом, состоящим из широко расходящихся микробных линий, чьи геномы содержат функционально сходные наборы генов, которые могут привести к возникновению согласованного единого метаболического исхода.…”

Bacterial species singled out from a diverse crowd

“…Yet, despite the incredible range of functions that different bacteria perform independently and in association with other living systems 3,4 , most microbes are similar in shape and indistinguishable under the microscope. Writing in Nature, Shi et al 5 present a method to tackle the major challenge of differentiating between the hundreds to thousands of bacterial species found in microbes' natural habitats.…”

“…A method to identify more than 1,000 bacterial species at high spatial resolution. Shi et al5 present their technique called high phylogenetic resolution microbiome mapping by fluorescence in situ hybridization (HiPR-FISH).…”