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Updated: Jun 13, 2026

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
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Published on: July 9, 2021

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在肠道组织微环境中进行宿主微生物组剖析的多omics空间框架

Bokai Zhu1,2,3, Yunhao Bai2,3, Yao Yu Yeo4

  • 1Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.

Nature communications
|January 31, 2025
PubMed
概括

微生物组绘图 (MicroCart) 提供了一种新的方法,可以在现场研究宿主微生物组相互作用. 这种空间的多组学框架揭示了在肠道炎症期间的动态免疫和微生物转移.

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Introduction to the Human Microbiota

Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity, and disease...
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The human microbiota begins developing at birth and undergoes continual change as we age. Infancy marks a critical period of microbial sensitivity, offering a “window of opportunity” during which beneficial microbes help mature the immune system. By age three, children typically develop a more stable and diverse microbial community. Newborns acquire microbes from their immediate environment; vaginal delivery favors maternal vaginal microbes, while cesarean births favor microbes from the skin...
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The Oral Microbiota

The oral microbiome includes a complex ecosystem comprising over 700 microbial species, identified through genomic sequencing and culture-based analyses to date. This community includes a core microbiome, found universally among individuals, and a variable component influenced by environmental factors such as diet, lifestyle, and host genetics. Site-specific conditions, including oxygen gradients, pH levels, and nutrient availability, determine the spatial distribution of these microorganisms...
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Microbiota of the Stomach and Small Intestine

The human gastrointestinal (GI) tract is characterized by distinct physicochemical conditions that shape its microbial communities. Among these, the stomach presents a particularly challenging environment for microbial colonization due to its highly acidic pH, ranging from 1 to 3. This extreme acidity effectively limits microbial density. However, certain acid-tolerant microorganisms are capable of surviving in this niche. Notably, Helicobacter pylori can colonize the gastric mucosa,...
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Microbiota of the Large Intestine

The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...