Human Microbiome 🦠

https://humanmicrobiome.substack.com/

Microbiome-related Inspirational Works

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Asnicar, Berry, Valdes, et al.

Nat Med, 27, 321–332 (2021)

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Gut micro-organisms associated with health, nutrition and dietary interventions

Asnicar, Manghi, Fackelmann, et al.

Nature, 650, 450–458 (2026)

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Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Buffie, Bucci, Stein, et al.

Nature, 517, 205–208 (2015)

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Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases

Co, Margalef-Català, Monack, Amieva

Nat Protoc, 16, 5171–5192 (2021)

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A metabolic pathway for bile acid dehydroxylation by the gut microbiome

Funabashi, Grove, Wang, et al.

Nature, 582, 566–570 (2020)

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Non-antibiotics disrupt colonization resistance against enteropathogens

Grießhammer, de la Cuesta-Zuluaga, Müller, et al.

Nature, 644, 497–505 (2025)

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Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium

Nature, 486, 207–214 (2012)

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Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

Ianiro, Punčochář, Karcher, et al.

Nat Med, 28, 1913–1923 (2022)

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Analysis of metagenomic data

Liu, Rodriguez, Munteanu, et al.

Nat Rev Methods Primers, 5, 5 (2025)

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Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price, Mahurkar, Rahnavard, et al.

Nature, 550, 61–66 (2017)

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Extensive impact of non-antibiotic drugs on human gut bacteria

Maier, Pruteanu, Kuhn, et al.

Nature, 555, 623–628 (2018)

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Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection

Menon R, Bhattarai SK, Crossette E, Prince AL, Olle B, Silber JL, Bucci V, Faith J, Norman JM

Nat Med, 31, 223–234 (2025)

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Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Paik, Yao, Zhang, et al.

Nature, 603, 907–912 (2022)

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Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer

Piccinno, Thompson, Manghi, et al.

Nat Med, 31, 2416–2429 (2025)

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Dissecting microbial communities with single-cell transcriptome analysis

Pountain, Yanai

Science, 389, eadp6252 (2025)

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Intestinal organoid cocultures with microbes

Puschhof, Pleguezuelos-Manzano, Martinez-Silgado, et al.

Nat Protoc, 16, 4633–4649 (2021)

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Bile salt hydrolase catalyses formation of amine-conjugated bile acids

Rimal, Collins, Tanes, et al.

Nature, 626, 859–863 (2024)

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Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians

Sato, Atarashi, Plichta, et al.

Nature, 599, 458–464 (2021)

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The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

Schluter, Djukovic, Taylor, et al.

Cell Host Microbe, 31, 1126–1139 (2023)

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Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Scholz, Ward, Pasolli, et al.

Nat Methods, 13, 435–438 (2016)

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Profiling the human intestinal environment under physiological conditions

Shalon, Culver, Grembi, et al.

Nature, 617, 581–591 (2023)

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Enterococci enhance Clostridioides difficile pathogenesis

Smith, Jenior, Keenan, et al.

Nature, 611, 780–786 (2022)

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Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

Theriot, Koenigsknecht, Carlson, et al.

Nat Commun, 5, 3114 (2014)

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A core gut microbiome in obese and lean twins

Turnbaugh, Hamady, Yatsunenko, et al.

Nature, 457, 480–484 (2009)

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The person-to-person transmission landscape of the gut and oral microbiomes

Valles-Colomer, Blanco-Míguez, Manghi, et al.

Nature, 614, 125–135 (2023)

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Long-read metagenomics reveals phage dynamics in the human gut microbiome

Wirbel, Hickey, Chang, et al.

Nature (2025)

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Using clusterProfiler to characterize multiomics data

Xu, Hu, Cai, et al.

Nat Protoc, 19, 3292–3320 (2024)

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Brief antibiotic use drives human gut bacteria towards low-cost resistance

Yaffe, Dethlefsen, Patankar, et al.

Nature, 641, 182–191 (2025)

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Microbiome-related Inspirational Works

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals

Gut micro-organisms associated with health, nutrition and dietary interventions

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Controlling the polarity of human gastrointestinal organoids to investigate epithelial biology and infectious diseases

A metabolic pathway for bile acid dehydroxylation by the gut microbiome

Non-antibiotics disrupt colonization resistance against enteropathogens

Structure, function and diversity of the healthy human microbiome

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

Analysis of metagenomic data

Strains, functions and dynamics in the expanded Human Microbiome Project

Extensive impact of non-antibiotic drugs on human gut bacteria

Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer

Dissecting microbial communities with single-cell transcriptome analysis

Intestinal organoid cocultures with microbes

Bile salt hydrolase catalyses formation of amine-conjugated bile acids

Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Profiling the human intestinal environment under physiological conditions

Enterococci enhance Clostridioides difficile pathogenesis

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

A core gut microbiome in obese and lean twins

The person-to-person transmission landscape of the gut and oral microbiomes

Long-read metagenomics reveals phage dynamics in the human gut microbiome

Using clusterProfiler to characterize multiomics data

Brief antibiotic use drives human gut bacteria towards low-cost resistance

Clostridioides difficile infection (CDI)

Immunotherapy Checkpoint Inhibition (ICI) Response

Colorectal Cancer (CRC)

Inflammatory Bowel Disease (IBD)

Microbiome-related Lab Publications

Discussion