Topics and Trends in Most Cited Gut microbiota and health Papers, Class of 2026

What topics and trends defined most-cited Gut microbiota and health research in the Class of 2026?

The Class of 2026 ranking in gut microbiota and health underscores a strong pivot toward microbiome-immune interactions. Fecal microbiota transplantation and immune checkpoint blockade remain central, while research is rapidly expanding into specific metabolites like indole-3-lactic acid and their roles in therapeutic response and disease modulation.

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Updated July 19, 2026

At a glance

Field: Gut microbiota and health
Cohort label: Class of 2026 (2024 publications)
Papers analyzed: 17221
Papers ranked: 20
Top topics in ranked papers: Fecal microbiota transplantation, Immune checkpoint blockade, Inflammatory bowel disease
Publication window: Jan 1, 2024 – Dec 31, 2024
Eligibility: Research articles; reviews excluded
Citation window: 18 months post-publication
18m citation range: 109–222
Data source: OpenAlex · Retrieved June 2026
License: CC BY 4.0

Rankings

20 papers ranked by 18-month citation count

#1 of 17,221

22218m citations

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

Martha Zepeda-Rivera et al.Nature202410.1038/s41586-024-07182-w

Susan Bullman, Christopher D. JohnstonFred Hutchinson Cancer Center, United States

Fusobacterium nucleatumColorectal cancerFusobacterium nucleatum subspecies animalisFna C1 cladeFna C2 cladeclosed genome sequencingpangenomic analysisCRC-enriched genetic factorstumor colonizationpathoadaptationColorectal adenomaMetabolomic profilingTumor microbiomeMetagenomic analysistumor-adjacent tissue comparisongastrointestinal tract colonizationcancer recurrencepatient prognosisoral cavity microbiomeclade bifurcation

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#2 of 17,221

20318m citations

EzBioCloud: a genome-driven database and platform for microbiome identification and discovery

Mauricio Chalita et al.INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY202410.1099/ijsem.0.006421

Mauricio ChalitaCJ Bioscience Inc, South Korea

EzBioCloud16S rRNA sequencinggenome sequence comparisonAverage nucleotide identityCore gene ANIbacterial core genesTaxonomic classificationNCBI Assembly Databasequality control protocolscandidate speciesphylotypesgenomospeciesspecies clustersvalidly published namesBacteria and Archaea classificationmicrobiome identificationwhole-genome assembliesunderrepresented lineages

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#3 of 17,221

18718m citations

Microbial metabolite enhances immunotherapy efficacy by modulating T cell stemness in pan-cancer

Dingjiacheng Jia et al.Cell202410.1016/j.cell.2024.02.022

Shujie Chen, Liangjing WangSecond Affiliated Hospital of Zhejiang University School of Medicine, China

Microbial metabolitesImmunotherapy responseT cell stemnessPan-cancer analysisTumor microbiomeImmune checkpoint blockademetabolite-immune axisCD8+ T cellsT cell exhaustionantitumor immunityT cell differentiationImmune modulationCancer immunotherapy

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#4 of 17,221

17518m citations

A core microbiome signature as an indicator of health

Guojun Wu et al.Cell202410.1016/j.cell.2024.09.019

Guojun WuRutgers, The State University of New Jersey, United States

Gut microbiomecore microbiomeMetagenomic datasetshigh-fiber dietary interventiontype 2 diabetesco-abundance networksstably correlated genome pairstwo competing guilds modelfiber fermentationbutyrate productionvirulence genesantibiotic resistancerandom forest modelsimmunotherapy outcome predictionguild-based approachsystems biologycase-control studies

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#5 of 17,221

16618m citations

Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway

Qixing Nie et al.Cell202410.1016/j.cell.2024.03.034

Yanxing Jia, Ming‐Hua Zheng, Yanli Pang, Jie Qiao, Changtao JiangPeking University, China

MASHGut microbiomesecondary bile acid3-succinylated cholic acidclick-chemistry-based enrichmentMAFLDBacteroides uniformisβ-lactamaseactivity-based protein purificationAkkermansia muciniphilalumen-restricted metaboliteBile acid-microbiota interactionsmicrobial-derived bile acids

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#6 of 17,221

16218m citations

Fusobacterium nucleatum facilitates anti-PD-1 therapy in microsatellite stable colorectal cancer

Xueliang Wang et al.Cancer Cell202410.1016/j.ccell.2024.08.019

Jun YuThe First Affiliated Hospital, China

Fusobacterium nucleatummicrosatellite stable colorectal cancerImmune checkpoint blockadeFecal microbiota transplantationButyratehistone deacetylase 3/8CD8+ T cellsTbx21 promoterH3K27 acetylationTBX21PD-1 transcriptional repressionCD8+ T cell exhaustionCD34+-humanized micebutyric acid-producing gene knockoutTumor microbiomeImmunotherapy resistanceimmunotherapy biomarker

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#7 of 17,221

13518m citations

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding

Gang Wang et al.Microbiome202410.1186/s40168-024-01750-y

Xiangfang ZengChina Agricultural University, China

Indole-3-lactic acidIndole-3-propionic acidIndole-3-acetic acidLactobacillustryptophan metabolismMicrobial metabolic interactionsintestinal inflammationMicrobiome modulationDSS-induced colitisIL-10−/− spontaneous colitisClostridiumacyl-CoA dehydrogenaseIndolelactate dehydrogenaseCitrobacter rodentiumDysbiosisHost-microbe interactionspostbioticsindole derivativestryptophan-metabolizing bacteria

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#8 of 17,221

13518m citations

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria

Chenhao Li et al.Cell202410.1016/j.cell.2024.03.014

Chenhao LiBroad Institute of MIT and Harvard, United States

Gut microbiomeMetabolomic profilingFramingham Heart Studycholesterol-metabolizing bacteriacholesterol metabolismmicrobial metabolismserum metabolitesmicrobial enzymesbile acidscoprostanolcardiovascular diseaseMetagenomic sequencingmetabolomicsHost-microbe interactions

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#9 of 17,221

12818m citations

Dubosiella newyorkensis modulates immune tolerance in colitis via the L-lysine-activated AhR-IDO1-Kyn pathway

Yanan Zhang et al.Nature Communications202410.1038/s41467-024-45636-x

Shu ZhuZhejiang University, China

Dubosiella newyorkensisClostridium innocuumDSS-induced colitisL-LysineAryl hydrocarbon receptor (AhR)Indoleamine 2,3-dioxygenasekynurenine pathwayTreg/Th17 balancedendritic cellstryptophan catabolismShort-chain fatty acidspropionatemucosal barrierimmune toleranceGnotobiotic miceInflammatory bowel disease

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#10 of 17,221

12818m citations

Bile acids modified by the intestinal microbiota promote colorectal cancer growth by suppressing CD8+ T cell effector functions

Jingjing Cong et al.Immunity202410.1016/j.immuni.2024.02.014

Wen Pan, Shu ZhuUniversity of Science and Technology of China, China

bile acidsGut microbiomeColorectal cancerCD8+ T cellsT cell effector functionsBile acid metabolismtumor immunityMicrobiome-cancer interactionsimmunosuppression

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#11 of 17,221

12618m citations

Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota

Anurag K Sinha, Martin F Laursen et al.Nature Microbiology202410.1038/s41564-024-01737-3

Anurag Kumar Sinha, Tine Rask LichtTechnical University of Denmark, Denmark

tryptophan metabolismGut microbiomeDietary fiberindoleIndole-3-lactic acidIndole-3-propionic acidEscherichia coliClostridium sporogenesBacteroides thetaiotaomicronthree-species defined communityMicrobial metabolic interactionsMonosaccharidescatabolite repressionchronic kidney diseasefermentable fibresFecal microbiota transplantationGnotobiotic micesubstrate-dependent regulationmetabolic interactions

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#12 of 17,221

12418m citations

Immunoregulatory role of the gut microbiota in inflammatory depression

Penghong Liu, Zhifen Liu et al.Nature Communications202410.1038/s41467-024-47273-w

Ning Sun, Kerang ZhangFirst Hospital of Shanxi Medical University, China

inflammatory depressionGut microbiometreatment-resistant depressionBacteroidesClostridiumShort-chain fatty acidsbutanoate metabolismFecal microbiota transplantationFMTClostridium butyricumIntestinal barrier functionneuroinflammationperipheral inflammatory factorscentral inflammatory factorsdepressive-like behaviorsanxiety-like behaviorsProbiotic therapySCFA-producing species

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#13 of 17,221

12218m citations

Wekemo Bioincloud: A user‐friendly platform for meta‐omics data analyses

Yunyun Gao et al.iMeta202410.1002/imt2.175

Yongxin LiuAgricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences, China

Wekemo BioincloudMulti-omicsmicrobiome data analysisbioinformatics platformhuman microbiomeenvironmental microbiomeMicrobiome compositionMicrobiome functionintercellular interactionsscalability challengesanalysis workflowsvisualization toolsvector output modificationpersonalized dashboard systemdata privacydata traceabilityuser-friendly interface

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#14 of 17,221

12118m citations

Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice

Kaili Fu et al.Cell202410.1016/j.cell.2024.01.004

Joseph J.�Y. Sung, Jun YuThe Chinese University of Hong Kong, China

Streptococcus anginosusgastric cancerchronic gastritisparietal cell atrophymucinous metaplasiadysplasiaGnotobiotic miceYTN16 GC cell allograftsgastric barrier functionTMPC surface proteinAnnexin A2ANXA2 receptorgastric epithelial cellsMAPK activationANXA2 knockoutTMPC-ANXA2-MAPK axisbacterial colonizationcarcinogen-induced gastric tumorigenesis

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#15 of 17,221

11718m citations

Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota

Huating Li, Lei Zhang, Jun Li, Qian Wu et al.Nature Metabolism202410.1038/s42255-024-00988-y

Huating Li, Xinyu Liu, Gianni Panagiotou, Aimin Xu, Weiping JiaShanghai Key Laboratory of Diabetes Mellitus, China

resistant starchweight lossGut microbiomeobesityinsulin resistanceBifidobacterium adolescentisbile acid profileIntestinal barrier functionlipid absorptiondietary fiber supplementationrandomized placebo-controlled crossover trialMicrobiome compositiondiet-induced obesityinflammationMetabolic diseaseoverweight

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#16 of 17,221

11718m citations

Engineered probiotic ameliorates ulcerative colitis by restoring gut microbiota and redox homeostasis

Peilin Guo et al.Cell Host & Microbe202410.1016/j.chom.2024.07.028

Yimin Cui, Guanghui Ma, Wei WeiChinese Academy of Sciences, China

Engineered probioticsulcerative colitisMicrobiome modulationredox homeostasisProbiotic therapyintestinal inflammationoxidative stressInflammatory bowel diseaseAntioxidant activitycolonic mucosaDysbiosisReactive oxygen species

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#17 of 17,221

11618m citations

A pan-cancer analysis of the microbiome in metastatic cancer

Thomas W Battaglia et al.Cell202410.1016/j.cell.2024.03.021

Emile E. VoestNetherlands Cancer Institute, Netherlands

Metastatic cancerTumor microbiomeMetagenomic sequencingorgan-specific microbial tropismanaerobic bacteriatumor hypoxiaMicrobial diversitytumor-infiltrating neutrophilsFusobacteriumImmunotherapy resistancelung cancerlongitudinal tumor samplingLongitudinal microbiome profilingPan-cancer analysismetastatic tumor biopsiesassembly-based metagenomicsImmune modulationImmunotherapy response

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#18 of 17,221

11618m citations

Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis

Shanshan Zhang, Qixing Nie, Yonggan Sun et al.Microbiome202410.1186/s40168-024-01896-9

Mingyong Xie, Shaoping NieNanchang University, China

β-glucanBacteroides uniformisLactobacillus johnsoniiIndole-3-lactic acidAryl hydrocarbon receptor (AhR)colitisDietary fiberMicrobial metabolic interactionsnicotinamideMulti-omicsLactobacillus abundanceβ-glucan degradationILA-AhR axisInflammatory bowel diseaseMicrobiome modulation

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#19 of 17,221

11418m citations

Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor

Yunjae Kim et al.Cell Host & Microbe202410.1016/j.chom.2024.06.010

Sang Hyoung Park, Sook Ryun Park, Sook Ryun ParkGwangju Institute of Science and Technology (GIST), South Korea

Fecal microbiota transplantationImmune checkpoint blockadeunresectable solid cancersMetastatic canceranti-PD-1 refractory cancersImmunotherapy resistancegut microbiome modulationFMT response enhancement

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#20 of 17,221

10918m citations

The gut commensal Blautia maintains colonic mucus function under low-fiber consumption through secretion of short-chain fatty acids

Sandra M Holmberg, Rachel H Feeney, Vishnu Prasoodanan P K et al.Nature Communications202410.1038/s41467-024-47594-w

Bjoern O. SchroederUmeå University, Sweden

Blautiacolonic mucus functionlow-fiber dietShort-chain fatty acidsFecal microbiota transplantationmucus growthBlautia coccoidespropionateacetateFfar2dietary fiber intakeCommensal bacteriamicrobe-mucus interactionex vivo mucus analysisSCFA receptor activation

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Topic trends

Dominant research themes and year-over-year shifts in Gut microbiota and health

What Topics Define the Class of 2026?

The Class of 2026 for gut microbiota and health is heavily defined by therapeutic interventions and their molecular underpinnings. Interventions such as fecal microbiota transplantation (FMT) and immune checkpoint blockade (ICB) dominate the landscape, reflecting a translational focus on modulating the microbiome to improve clinical outcomes, particularly in colorectal cancer and inflammatory bowel disease. Mechanistic studies are increasingly prominent, with a strong emphasis on short-chain fatty acids and tryptophan metabolism. Researchers are actively investigating how specific microbial metabolites, like indole-3-lactic acid, interact with host pathways such as the aryl hydrocarbon receptor (AhR) to regulate intestinal barrier function and immune tolerance. This highlights a maturation in the field from broad compositional surveys toward precise, multi-omics characterization of host-microbe interactions and their therapeutic potential.

How Did Topics Shift from the Class of 2025 to the Class of 2026?

Comparing the Class of 2025 to 2026 reveals a significant shift from broad microbiome profiling to highly specific metabolic and disease-focused investigations. The most dramatic rise was seen in ulcerative colitis and DSS-induced colitis, indicating intensified research into inflammatory disease models. Specific metabolites also surged in focus; indole-3-lactic acid saw a massive four-fold increase in frequency, reflecting growing interest in tryptophan metabolism and its immunomodulatory effects. Dietary fiber and its role in shaping the microbiome also emerged as rapidly trending areas. Conversely, broader terms like colorectal cancer and general metagenomic sequencing experienced relative declines or stabilization, suggesting the field is moving past initial exploratory sequencing and broad disease associations toward defining the precise molecular mechanisms and specific bacterial strains (like Bacteroides and Clostridium) that drive health and disease.

Methodology

PRI identifies high-impact research using a transparent, topic-agnostic framework applied consistently across scientific domains. Bibliographic records are drawn from OpenAlex, including publication dates, citation relationships, and document types.

This ranking covers the Class of 2026 cohort: journal articles published in 2024. Reviews and other non-article document types are excluded to ensure comparability.

Research impact is quantified with an 18-month post-publication citation window—the number of citing works published within 18 months of each paper's publication date. This metric captures early impact while controlling for publication age.

An LLM-based relevance classifier then reviews each candidate's title and abstract to confirm substantive alignment with the target domain. Only papers classified as relevant appear in the final ranking.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459

Full methodology GitHub bioRxiv preprint

Cite this ranking

Pepkio Research Index (PRI). Topics and Trends in Most Cited Gut microbiota and health Papers, Class of 2026. https://pri.pepkio.com/top-papers/gut-microbiota-and-health/2026. Accessed 2026-07-19.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459