Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection DOI Creative Commons
Bruce Wang, Aaron E. Lin, Jiayi Yuan

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(10), P. 1846 - 1862

Published: Aug. 31, 2023

Abstract Bacterial populations are highly adaptive. They can respond to stress and survive in shifting environments. How the behaviours of individual bacteria vary during stress, however, is poorly understood. To identify characterize rare bacterial subpopulations, technologies for single-cell transcriptional profiling have been developed. Existing approaches show some degree limitation, example, terms number cells or transcripts that be profiled. Due part these limitations, few conditions studied with tools. Here we develop massively-parallel, multiplexed, microbial sequencing (M3-seq)—a RNA-sequencing platform pairs combinatorial cell indexing post hoc rRNA depletion. We M3-seq profile from different species under a range single experiments. then apply hundreds thousands cells, revealing insights into bet-hedging associated responses characterizing phage infection.

Language: Английский

The microbiome and human cancer DOI
Gregory D. Sepich‐Poore, Laurence Zitvogel, Ravid Straussman

et al.

Science, Journal Year: 2021, Volume and Issue: 371(6536)

Published: March 25, 2021

Microbial roles in cancer formation, diagnosis, prognosis, and treatment have been disputed for centuries. Recent studies provocatively claimed that bacteria, viruses, and/or fungi are pervasive among cancers, key actors immunotherapy, engineerable to treat metastases. Despite these findings, the number of microbes known directly cause carcinogenesis remains small. Critically evaluating building frameworks such evidence light modern biology is an important task. In this Review, we delineate between causal complicit trace common themes their influence through host's immune system, herein defined as immuno-oncology-microbiome axis. We further review intratumoral approaches manipulate gut or tumor microbiome while projecting next phase experimental discovery.

Language: Английский

Citations

895
Spatial transcriptomics of planktonic and sessile bacterial populations at single-cell resolution DOI
Daniel Dar,

Nina Dar,

Long Cai

et al.

Science, Journal Year: 2021, Volume and Issue: 373(6556)

Published: Aug. 12, 2021

Capturing the heterogeneous phenotypes of microbial populations at relevant spatiotemporal scales is highly challenging. Here, we present par-seqFISH (parallel sequential fluorescence in situ hybridization), a transcriptome-imaging approach that records gene expression and spatial context within microscale assemblies single-cell molecule resolution. We applied this to opportunistic pathogen Pseudomonas aeruginosa, analyzing about 600,000 individuals across dozens conditions planktonic biofilm cultures. identified numerous metabolic- virulence-related transcriptional states emerged dynamically during growth, as well spatially resolved metabolic heterogeneity sessile populations. Our data reveal distinct physiological can coexist same just several micrometers away, underscoring importance microenvironment. results illustrate complex dynamics new way studying them high

Language: Английский

Citations

211
Bacteria in cancer initiation, promotion and progression DOI
Geniver El Tekle, Wendy S. Garrett

Nature reviews. Cancer, Journal Year: 2023, Volume and Issue: 23(9), P. 600 - 618

Published: July 3, 2023

Language: Английский

Citations

156
The gut microbiota and its biogeography DOI
Giselle McCallum, Carolina Tropini

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(2), P. 105 - 118

Published: Sept. 22, 2023

Language: Английский

Citations

140
Microbiota in Tumors: From Understanding to Application DOI
Yifan Xie, Feng Xie, Xiaoxue Zhou

et al.

Advanced Science, Journal Year: 2022, Volume and Issue: 9(21)

Published: May 23, 2022

Microbes with complex functions have been found to be a potential component in tumor microenvironments. Due their low biomass and other obstacles, intratumor microbiota is poorly understood. Mucosal sites normal adjacent tissues are important sources of microbiota, while hematogenous spread also leads the invasion microbes. Intratumor affects progression tumors through several mechanisms, such as DNA damage, activation oncogenic pathways, induction immunosuppression, metabolization drugs. Notably, different types tumors, composition abundance highly heterogeneous may play roles tumors. Because concern this field, techniques omics immunological methods used study microbiota. Here, recent progress field reviewed, including related heterogeneity. Techniques that can discussed. Moreover, research summarized into development strategies antitumor treatment prospects for possible future field.

Language: Английский

Citations

120
Oral polymicrobial communities: Assembly, function, and impact on diseases DOI Creative Commons
George Hajishengallis, Richard J. Lamont, Hyun Koo

et al.

Cell Host & Microbe, Journal Year: 2023, Volume and Issue: 31(4), P. 528 - 538

Published: March 17, 2023

Language: Английский

Citations

81
Single-cell approaches in human microbiome research DOI Creative Commons
Verónica Lloréns‐Rico, Joshua A. Simcock, Geert Huys

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(15), P. 2725 - 2738

Published: July 1, 2022

Language: Английский

Citations

78
Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview DOI Creative Commons
Ayomide Emmanuel Fadiji, Ajar Nath Yadav, Gustavo Santoyo

et al.

Microbiological Research, Journal Year: 2023, Volume and Issue: 271, P. 127368 - 127368

Published: March 22, 2023

Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth development. stressors like drought excessive heat are expected occur more frequently in the future due climate change, which would reduce yields of important crops maize, wheat, rice may jeopardize food security human populations. The microbiomes varied taxonomically organized microbial community that is connected plants. By supplying nutrients water plants, regulating their physiology metabolism, microbiota helps plants develop tolerate abiotic stresses, can boost crop yield under stresses. In this present study, with emphasis on temperature, salt, stress, we describe current findings how stresses impact microbiomes, microbe-microbe interactions, plant-microbe interactions as way microorganisms affect metabolism plant. We also explore crucial measures must be taken applying practices faced

Language: Английский

Citations

67
Spatial metatranscriptomics resolves host–bacteria–fungi interactomes DOI Creative Commons
Sami Saarenpää, Or Shalev, Haim Ashkenazy

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(9), P. 1384 - 1393

Published: Nov. 20, 2023

The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks spatial patterns. Existing technology does not allow simultaneous investigation between a multitude its colonizing microorganisms, which limits our understanding host-microorganism within plant or animal tissue. Here we present metatranscriptomics (SmT), sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for transcriptome- microbiome-wide characterization tissues 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as model system, find tissue-scale bacterial fungal hotspots. By network analysis, study inter- intrakingdom well response to microbial provides an answering fundamental questions on host-microbiome interplay.

Language: Английский

Citations

52
Spatial host–microbiome sequencing reveals niches in the mouse gut DOI Creative Commons

Britta Lötstedt,

Martin Stražar, Ramnik J. Xavier

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(9), P. 1394 - 1403

Published: Nov. 20, 2023

Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network cells microbes forming tight niche that prevents pathogen colonization supports host-microbiome symbiosis. Characterizing these networks at high molecular cellular resolution is crucial for understanding homeostasis disease. Here we present spatial sequencing (SHM-seq), an all-sequencing-based approach captures tissue histology, polyadenylated RNAs bacterial 16S sequences directly from by modifying spatially barcoded glass surfaces to enable simultaneous capture host transcripts hypervariable regions ribosomal RNA. We applied our mouse gut model system, used deep learning data mapping detected niches defined composition microbial geography. show subpopulations express specific gene programs in different microenvironments characteristic regional commensal bacteria impact host-bacteria interactions. SHM-seq should enhance study native host-microbe interactions health

Language: Английский

Citations

51