Alistipes onderdonkii subsp. onderdonkii KCTC 15237 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from human abdominal abscess.
Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria| @ref 20215 |
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Last LPSN update
2026-05-29 08:28:11 |
| Domain Bacteria |
| Phylum Bacteroidota |
| Class Bacteroidia |
| Order Bacteroidales |
| Family Rikenellaceae |
| Genus Alistipes |
| Species Alistipes onderdonkii subsp. onderdonkii |
| Full scientific name Alistipes onderdonkii subsp. onderdonkii (Song et al. 2006) Sakamoto et al. 2020 |
| BacDive ID | Other strains from Alistipes onderdonkii subsp. onderdonkii (2) | Type strain |
|---|---|---|
| 158110 | A. onderdonkii subsp. onderdonkii H3_19, DSM 108231 | |
| 158111 | A. onderdonkii subsp. onderdonkii H6_8, DSM 108265 |
| @ref | Name | Growth | Medium link | Composition | |
|---|---|---|---|---|---|
| 7936 | COLUMBIA BLOOD AGAR (DSMZ Medium 429) | Medium recipe at MediaDive  | Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base | ||
| 7936 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | Medium recipe at MediaDive | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
| 31803 | Observationaggregates in chains |
| @ref | Chebi-ID | Metabolite | Utilization activity | Kind of utilization tested | |
|---|---|---|---|---|---|
| 68380 | 16024 ChEBI | D-mannose | + | fermentation | from API rID32A |
| 31803 | 4853 ChEBI | esculin | + | hydrolysis | |
| 68380 | 29985 ChEBI | L-glutamate | - | degradation | from API rID32A |
| 31803 | 37684 ChEBI | mannose | + | carbon source | |
| 68380 | 17632 ChEBI | nitrate | - | reduction | from API rID32A |
| 31803 | 16634 ChEBI | raffinose | + | carbon source | |
| 68380 | 16634 ChEBI | raffinose | + | fermentation | from API rID32A |
| 68380 | 27897 ChEBI | tryptophan | + | energy source | from API rID32A |
| 68380 | 16199 ChEBI | urea | - | hydrolysis | from API rID32A |
| @ref | Value | Activity | Ec | |
|---|---|---|---|---|
| 68380 | alanine arylamidase | + | 3.4.11.2 | from API rID32A |
| 68380 | alkaline phosphatase | + | 3.1.3.1 | from API rID32A |
| 68380 | alpha-arabinosidase | - | 3.2.1.55 | from API rID32A |
| 68380 | alpha-fucosidase | - | 3.2.1.51 | from API rID32A |
| 68380 | alpha-galactosidase | + | 3.2.1.22 | from API rID32A |
| 68380 | alpha-glucosidase | + | 3.2.1.20 | from API rID32A |
| 68380 | beta-galactosidase | + | 3.2.1.23 | from API rID32A |
| 68380 | beta-Galactosidase 6-phosphate | - | from API rID32A | |
| 68380 | beta-glucosidase | - | 3.2.1.21 | from API rID32A |
| 68380 | beta-glucuronidase | - | 3.2.1.31 | from API rID32A |
| 68380 | glutamate decarboxylase | - | 4.1.1.15 | from API rID32A |
| 68380 | glutamyl-glutamate arylamidase | + | from API rID32A | |
| 68380 | glycin arylamidase | - | from API rID32A | |
| 68380 | histidine arylamidase | - | from API rID32A | |
| 68380 | L-arginine arylamidase | - | from API rID32A | |
| 68380 | leucine arylamidase | - | 3.4.11.1 | from API rID32A |
| 68380 | leucyl glycin arylamidase | + | 3.4.11.1 | from API rID32A |
| 68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 | from API rID32A |
| 68380 | phenylalanine arylamidase | - | from API rID32A | |
| 68380 | proline-arylamidase | - | 3.4.11.5 | from API rID32A |
| 68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 | from API rID32A |
| 68380 | serine arylamidase | - | from API rID32A | |
| 68380 | tryptophan deaminase | + | 4.1.99.1 | from API rID32A |
| 68380 | tyrosine arylamidase | - | from API rID32A | |
| 68380 | urease | - | 3.5.1.5 | from API rID32A |
| Cat1 | Cat2 | Cat3 | |
|---|---|---|---|
| #Host | #Human | - | |
| #Host Body-Site | #Other | #Abdomen | |
| #Host Body-Site | #Other | #Abscess | |
| #Infection | #Patient | - |
| @ref | Sample type | Host species | Sampling date | Geographic location | Country | Country ISO 3 Code | Continent | |
|---|---|---|---|---|---|---|---|---|
| 7936 | human abdominal abscess | Homo sapiens | USA | USA | North America | |||
| 58400 | Human abdominal abscess | Homo sapiens | 1989 | Los Angeles | USA | USA | North America | |
| 67770 | Human specimens | Homo sapiens | ||||||
| 67771 | From human abdominal abscess | Homo sapiens | USA | USA | North America |
Global distribution of 16S sequence AY974071 (>99% sequence identity) for Alistipes onderdonkii subclade from Microbeatlas 
 Aquatic Samples |
5936 |
 Soil Samples |
1356 |
 Animal Samples |
169152 |
 Plant Samples |
565 |
| Total Samples | 177009 |
| @ref | Description | Assembly level | INSDC accession | BV-BRC accession | IMG accession | NCBI tax ID | Score | |
|---|---|---|---|---|---|---|---|---|
| 66792 | ASM2514528v1 assembly for Alistipes onderdonkii DSM 19147 | complete | GCA_025145285   | 328813.144  | 8079342933  | 328813 | 98.67 | |
| 67770 | ASM37450v1 assembly for Alistipes onderdonkii WAL 8169 = DSM 19147 | scaffold | GCA_000374505 | 1120974.3 | 2517572213 | 1203611 | 72.68 |
| Topic | Title | Authors | Journal | DOI | Year | |
|---|---|---|---|---|---|---|
| Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice. | Coe GL, Krout IN, Munro-Ehrlich M, Beamish CR, Vorojeikina D, Colman DR, Boyd EJ, Walk ST, Rand MD. | Arch Toxicol | 10.1007/s00204-023-03548-7 | 2023 | | |
| Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. | Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. | Nat Commun | 10.1038/s41467-023-39121-0 | 2023 | | |
| Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma. | Zhang J, Yang J, Luo J, Wu W, Luo H, Wei W, Lyu H, Wang Y, Yi H, Zhang Y, Fan Z, Lyu H, Kanakaveti VP, Qin B, Yuan P, Yang R, Zhang H, Zuo T, Felsher DW, Lee MH, Li K. | Nat Commun | 10.1038/s41467-025-58407-z | 2025 | | |
| Metabolism | Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets. | Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P. | Sci Rep | 10.1038/s41598-017-10369-z | 2017 | |
| Metabolism | A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1. | Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR. | Cell Host Microbe | 10.1016/j.chom.2021.07.013 | 2021 | |
| Evidence of extensive DNA transfer between bacteroidales species within the human gut. | Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE. | mBio | 10.1128/mbio.01305-14 | 2014 | | |
| Design, construction, and in vivo augmentation of a complex gut microbiome. | Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA. | Cell | 10.1016/j.cell.2022.08.003 | 2022 | | |
| Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. | Coyne MJ, Roelofs KG, Comstock LE. | BMC Genomics | 10.1186/s12864-016-2377-z | 2016 | | |
| Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice. | Li X, He N, Wang H, Wu Z, Wang M, Liang H, Xiao L, Yang Z, Li C, Xu P, Dai T, Li S, Zou Y. | J Appl Microbiol | 10.1093/jambio/lxaf119 | 2025 | | |
| Enzymology | Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights. | Kuzmichenko P, Fedorov D, Galeeva J, Postoeva A, Krieger E, Kudryavtsev A, Pavlenko A, Vvedensky A, Starikova E, Govorun V, Ilina E. | Sci Rep | 10.1038/s41598-025-26617-6 | 2025 | |
| Causal Effects of Gut Microbiome on Tinnitus: A Mendelian Randomization Study. | Zeng Q, Xie W, Dong H, Liu X, Shao S, Chen L, Zhang W. | J Multidiscip Healthc | 10.2147/jmdh.s525502 | 2025 | | |
| Immunocytes Mediate the Effects of Gut Microbiome on Inflammatory Bowel Disease: Insights From a Mendelian Randomization Study. | He L, Wei J, Li Z, Guo S, Lin S, Wang T, Chen L. | Mediators Inflamm | 10.1155/mi/9956259 | 2025 | | |
| Pathogenicity | Body mass index distinctly modulates the associations between Alistipes and CRP/IL-6 in metabolic and lupus inflammatory features. | Chero-Sandoval L, Higuera-Gomez A, de Cuevillas B, Castejon R, Martinez-Urbistondo M, Mellor-Pita S, Moreno-Torres V, de Luis D, Cuevas-Sierra A, Martinez JA. | PLoS One | 10.1371/journal.pone.0335452 | 2025 | |
| Pathogenicity | Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets. | Haque S, Bantun F, Jalal NA, Faidah H, Babalghith AO, Alobaidy MA, Aldairi AF, Ahmad F. | Gut Pathog | 10.1186/s13099-025-00712-5 | 2025 | |
| From Tooth to Phalanx: The First Reported Case of Porphyromonas endodontalis Causing Osteomyelitis of the Proximal Phalanx. | Korah H, Popp M, Bercu C, Berger A. | Eplasty | 2025 | | ||
| The causal association between gut microbiota and postpartum depression: a two-sample Mendelian randomization study. | Jin W, Li B, Wang L, Zhu L, Chai S, Hou R. | Front Microbiol | 10.3389/fmicb.2024.1415237 | 2024 | | |
| Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling. | Charalambous H, Brown C, Vogazianos P, Katsaounou K, Nikolaou E, Stylianou I, Papageorgiou E, Vraxnos D, Aristodimou A, Chi J, Costeas P, Shammas C, Apidianakis Y, Antoniades A. | Thorac Cancer | 10.1111/1759-7714.70075 | 2025 | | |
| Metagenome-wide association study of gut microbiome features for myositis. | Li Y, Xu J, Hong Y, Li Z, Xing X, Zhufeng Y, Lu D, Liu X, He J, Li Y, Sun X. | Clin Immunol | 10.1016/j.clim.2023.109738 | 2023 | | |
| Phylogeny | Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis. | Hasan R, Bose S, Roy R, Paul D, Rawat S, Nilwe P, Chauhan NK, Choudhury S. | Arch Microbiol | 10.1007/s00203-022-02954-2 | 2022 | |
| Phylogeny | Distinct gut microbial species, but not phylum-to-genus composition, associate with insulin resistance: a unique perspective from the Kazakh population. | Abildinova GZ, Benberin VV, Vochshenkova TA, Mussin NM, Afshar A, Tamadon A. | Front Microbiol | 10.3389/fmicb.2025.1683885 | 2025 | |
| Machine learning prediction of obesity-associated gut microbiota: identifying Bifidobacterium pseudocatenulatum as a potential therapeutic target. | Wu H, Li Y, Jiang Y, Li X, Wang S, Zhao C, Yang X, Chang B, Yang J, Qiao J. | Front Microbiol | 10.3389/fmicb.2024.1488656 | 2024 | | |
| Pathogenicity | Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds. | Huminska-Lisowska K, Michalowska-Sawczyn M, Kosciolek T, Labaj PP, Kochanowicz A, Mieszkowski J, Proia P, Cieszczyk P, Zielinska K. | Sci Rep | 10.1038/s41598-025-99485-9 | 2025 | |
| Functional Outcome Prediction of Acute Ischemic Stroke Based on the Oral and Gut Microbiota. | Liang J, Ren Y, Zheng Y, Lin X, Song W, Zhu J, Zhang X, Zhou H, Wu Q, He Y, Yin J. | Mol Neurobiol | 10.1007/s12035-024-04618-2 | 2025 | | |
| Enzymology | Novel Endo-beta-N-Acetylglucosaminidases Derived from Human Fecal Samples Selectively Release N-Glycans from Model Glycoproteins. | Bolino M, Haththotuwe Gamage N, Duman H, Abiodun O, De Mello AS, Karav S, Frese SA. | Foods | 10.3390/foods14081288 | 2025 | |
| Genetics | Metagenomic analysis of gut microbiome reveals a dynamic change in Alistipes onderdonkii in the preclinical model of pancreatic cancer, suppressing its proliferation. | Lee K, Oh HJ, Kang MS, Kim S, Ahn S, Kim MJ, Kim SW, Chang S. | Appl Microbiol Biotechnol | 10.1007/s00253-021-11617-z | 2021 | |
| The gut microbiota-aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol-rich extracts from Sanghuangporus. | Zhong S, Sun YQ, Huo JX, Xu WY, Yang YN, Yang JB, Wu WJ, Liu YX, Wu CM, Li YG. | Imeta | 10.1002/imt2.180 | 2024 | | |
| Exploring the Relationship between MicroRNAs, Intratumoral Microbiota, and Breast Cancer Progression in Patients with and without Metastasis. | Laborda-Illanes A, Aranega-Martin L, Sanchez-Alcoholado L, Boutriq S, Plaza-Andrades I, Peralta-Linero J, Garrido Ruiz G, Pajares-Hachero B, Alvarez M, Alba E, Gonzalez-Gonzalez A, Queipo-Ortuno MI. | Int J Mol Sci | 10.3390/ijms25137091 | 2024 | | |
| Genetics | Gut microbiome and major depressive disorder: insights from two-sample Mendelian randomization. | Zhao Q, Baranova A, Cao H, Zhang F. | BMC Psychiatry | 10.1186/s12888-024-05942-6 | 2024 | |
| Phylogeny | First description of abdominal infection due to Alistipes onderdonkii. | Cobo F, Foronda C, Perez-Carrasco V, Martin-Hita L, Garcia-Salcedo JA, Navarro-Mari JM. | Anaerobe | 10.1016/j.anaerobe.2020.102283 | 2020 | |
| Fecal microbiota transplantation treatment for type 1 diabetes mellitus with malnutrition: a case report. | Xie YC, Jing XB, Chen X, Chen LZ, Zhang SH, Cai XB. | Ther Adv Chronic Dis | 10.1177/20406223221117449 | 2022 | | |
| Metabolism | High-fat diet promotes gestational diabetes mellitus through modulating gut microbiota and bile acid metabolism. | Yao L, Zhou X, Jiang X, Chen H, Li Y, Xiong X, Tang Y, Zhang H, Qiao P. | Front Microbiol | 10.3389/fmicb.2024.1480446 | 2024 | |
| Gut microbial signature in lung cancer patients highlights specific taxa as predictors for durable clinical benefit. | Haberman Y, Kamer I, Amir A, Goldenberg S, Efroni G, Daniel-Meshulam I, Lobachov A, Daher S, Hadar R, Gantz-Sorotsky H, Urban D, Braun T, Bar J. | Sci Rep | 10.1038/s41598-023-29136-4 | 2023 | | |
| Oral administration of the commensal Alistipes onderdonkii prolongs allograft survival. | Li Z, Rasic M, Kwan M, Sepulveda M, McIntosh C, Shastry V, Chen L, Finn P, Perkins D, Alegre ML. | Am J Transplant | 10.1016/j.ajt.2022.11.011 | 2023 | | |
| The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond. | Fagunwa O, Davies K, Bradbury J. | Nutrients | 10.3390/nu16070942 | 2024 | | |
| Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism. | Kwan SY, Gonzales KA, Jamal MA, Stevenson HL, Tan L, Lorenzi PL, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Jenq RR, Beretta L. | Gut Microbes | 10.1080/19490976.2024.2399260 | 2024 | | |
| Deciphering gut microbiome patterns from host preferences and microbial interactions in healthy Korean individuals. | Hong S, Lim MY, Chung WH, Shin JH, Nam YD. | BMC Biol | 10.1186/s12915-025-02291-y | 2025 | | |
| Genetics | Early-life gut microbiome maturity regulates blood-brain barrier and cognitive development. | Zemmel ZM, Fan X, Yu Y, Markiewicz E, Tsai HM, Lu L, Little JC, Ramaswamy R, Andrews B, Claud EC, Lu J. | Gut Microbes | 10.1080/19490976.2025.2551879 | 2025 | |
| Nutraceutical blends predict enhanced health via microbiota reshaping improving cytokines and life quality: a Brazilian double-blind randomized trial. | Santamarina AB, de Freitas JA, Franco LAM, Nehmi-Filho V, Fonseca JV, Martins RC, Turri JA, da Silva BFRB, Fugi BEI, da Fonseca SS, Gusmao AF, Olivieri EHR, de Souza E, Costa S, Sabino EC, Otoch JP, Pessoa AFM. | Sci Rep | 10.1038/s41598-024-61909-3 | 2024 | | |
| Phylogeny | Gut microbiome profile of Chinese hypertension patients with and without type 2 diabetes mellitus. | Ding H, Xu Y, Cheng Y, Zhou H, Dong S, Wu J, Lv J, Hu X, Tang O. | BMC Microbiol | 10.1186/s12866-023-02967-x | 2023 | |
| Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis. | Cao J, He Q, Zhang M, Zhou R, Feng C. | Pol J Microbiol | 10.33073/pjm-2025-011 | 2025 | | |
| Phylogeny | Gut Microbiome Dysbiosis in Patients with Pemphigus and Correlation with Pathogenic Autoantibodies. | Li SZ, Wu QY, Fan Y, Guo F, Hu XM, Zuo YG. | Biomolecules | 10.3390/biom14070880 | 2024 | |
| What Is the Role of the Gut Microbiota in Anastomotic Leakage After Colorectal Resection? A Scoping Review of Clinical and Experimental Studies. | Lianos GD, Frountzas M, Kyrochristou ID, Sakarellos P, Tatsis V, Kyrochristou GD, Bali CD, Gazouli M, Mitsis M, Schizas D. | J Clin Med | 10.3390/jcm13226634 | 2024 | | |
| Lactobacillus murinus Reduces Susceptibility to Secondary MRSA Infection in IAV-Infected Mice Through Promoting a T Cell-Independent IgA Response. | Chen Q, Lin Y, Wang K, Li J, Li P, Song H. | Microorganisms | 10.3390/microorganisms13071709 | 2025 | | |
| Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia. | Zeng L, Yu B, Zeng P, Duoji Z, Zuo H, Lian J, Yang T, Dai Y, Feng Y, Yu P, Yang J, Yang S, Dou Q. | NPJ Biofilms Microbiomes | 10.1038/s41522-025-00721-x | 2025 | | |
| Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting. | Rasoulimehrabani H, Khadem S, Hodzic A, Philipp M, Gallo R, Nikolov G, Seneca J, Ramesmayer J, Sivulic P, Berry D. | Microbiome Res Rep | 10.20517/mrr.2025.29 | 2025 | | |
| Pathogenicity | Nutraceutical Capsules LL1 and Silymarin Supplementation Act on Mood and Sleep Quality Perception by Microbiota-Gut-Brain Axis: A Pilot Clinical Study. | Santamarina AB, Nehmi Filho V, Freitas JA, Franco LAM, Fonseca JV, Martins RC, Turri JAO, Silva BFRBD, Gusmao AF, Olivieri EHR, Otoch JP, Pessoa AFM. | Nutrients | 10.3390/nu16183049 | 2024 | |
| Pathogenicity | Potential roles of the interactions between gut microbiota and metabolites in LPS-induced intrauterine inflammation (IUI) and associated preterm birth (PTB). | Jia B, Tang L, Liu H, Chen W, Chen Q, Zhong M, Yin A. | J Transl Med | 10.1186/s12967-023-04603-8 | 2024 | |
| Phylogeny | Relationship Between Gut Microbiota and the Clinical Course of COVID-19 Disease. | Jonjic A, Dolanc I, Slivsek G, Bockor L, Tarle M, Mustapic S, Kmet M, Orehovec B, Kucan Brlic P, Cokaric Brdovcak M, Obad A, Walenta M, Drazic I, Bilic-Zulle L, Luksic I, Bulic N, Goessler W, Jonjic S, Coklo M, Zucko J. | Viruses | 10.3390/v17040520 | 2025 | |
| Clinical effectiveness of fecal microbial transplantation for metabolic syndrome: Advances in clinical efficacy and multi-omics research. | Wang H, Tian J, Mi J. | Curr Res Microb Sci | 10.1016/j.crmicr.2025.100415 | 2025 | | |
| Phylogeny | The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery. | Yang Y, Zhou HY, Zhou GM, Chen J, Ming R, Zhang D, Jiang HW. | Front Microbiol | 10.3389/fmicb.2024.1494049 | 2024 | |
| A Preliminary Study Exploring the Relationship between Occupational Health Hazards and Gut Microbiota among Firefighters. | Yoo JY, McSkimming D, Rajan K, Sarkar A, Labbe N, Groer M, Menon U. | Life (Basel) | 10.3390/life13091928 | 2023 | | |
| Pathogenicity | Inflammation Mediated by Gut Microbiome Alterations Promotes Lung Cancer Development and an Immunosuppressed Tumor Microenvironment. | Rahal Z, Liu Y, Peng F, Yang S, Jamal MA, Sharma M, Moreno H, Damania AV, Wong MC, Ross MC, Sinjab A, Zhou T, Chen M, Tarifa Reischle I, Feng J, Chukwuocha C, Tang E, Abaya C, Lim JK, Leung CH, Lin HY, Deboever N, Lee JJ, Sepesi B, Gibbons DL, Wargo JA, Fujimoto J, Wang L, Petrosino JF, Ajami NJ, Jenq RR, Moghaddam SJ, Cascone T, Hoffman K, Kadara H. | Cancer Immunol Res | 10.1158/2326-6066.cir-24-0469 | 2024 | |
| Phylogeny | Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection. | Lin X, Lin C, Li X, Yao F, Guo X, Wang M, Zeng M, Yuan Y, Xie Q, Huang X, Jiao X. | J Microbiol | 10.1007/s12275-024-00190-5 | 2024 | |
| Genetics | Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis. | Luo Y, Sheikh TMM, Li X, Yuan Y, Yao F, Wang M, Guo X, Wu J, Shafiq M, Xie Q, Jiao X. | Virulence | 10.1080/21505594.2024.2428843 | 2024 | |
| Gut microbiota, physical activity and/or metabolic markers in healthy individuals - towards new biomarkers of health. | Myhrstad MCW, Ruud E, Gaundal L, Gjovaag T, Rud I, Retterstol K, Ulven SM, Holven KB, Koehler K, Telle-Hansen VH. | Front Nutr | 10.3389/fnut.2024.1438876 | 2024 | | |
| Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial. | Block MS, Nelson GD, Chen J, Johnson S, Yang L, Flotte TJ, Grewal EP, McWilliams RR, Kottschade LA, Domingo-Musibay E, Markovic SN, Dimou A, Montane HN, Piltin MA, Price DL, Khariwala SS, Hui JYC, Erskine CL, Strand CA, Zahrieh D, Dong H, Hieken TJ. | J Immunother Cancer | 10.1136/jitc-2025-011706 | 2025 | | |
| The relative abundance of fecal bacterial species belonging to the Firmicutes and Bacteroidetes phyla is related to plasma levels of bile acids in young adults. | Osuna-Prieto FJ, Xu H, Ortiz-Alvarez L, Di X, Kohler I, Jurado-Fasoli L, Rubio-Lopez J, Plaza-Diaz J, Vilchez-Vargas R, Link A, Gil A, Ruiz JR, Rensen PCN, Martinez-Tellez B. | Metabolomics | 10.1007/s11306-023-02016-8 | 2023 | | |
| Longitudinal analysis of gut microbiome and metabolome correlates of response and toxicity with idecabtagene vicleucel. | Saha S, Rehman L, Rehman A, Darbaniyan F, Weber DM, Becnel M, Gaballa M, Thomas SK, Lee HC, Chang CC, Arora R, Menges M, Corallo S, Davila ML, Locke FL, Tanner MR, Neelapu SS, Shpall EJ, Flowers CR, Orlowski RZ, Jenq RR, Jain MD, Peterson C, Hansen DK, Saini NY, Patel KK. | Blood Adv | 10.1182/bloodadvances.2024014476 | 2025 | | |
| Genetics | A Metagenome-Wide Association Study of the Gut Microbiome and Metabolic Syndrome. | Qin Q, Yan S, Yang Y, Chen J, Li T, Gao X, Yan H, Wang Y, Wang J, Wang S, Ding S. | Front Microbiol | 10.3389/fmicb.2021.682721 | 2021 | |
| Metabolism | Association of Subjective and Objective Measures of Sleep With Gut Microbiota Composition and Diversity in Older Men: The Osteoporotic Fractures in Men Study. | Estaki M, Langsetmo L, Shardell M, Mischel A, Jiang L, Zhong Y, Kaufmann C, Knight R, Stone K, Kado D. | J Gerontol A Biol Sci Med Sci | 10.1093/gerona/glad011 | 2023 | |
| Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer. | Queen J, Cing Z, Minsky H, Nandi A, Southward T, Ferri J, McMann M, Iyadorai T, Vadivelu J, Roslani A, Loke MF, Wanyiri J, White JR, Drewes JL, Sears CL. | NPJ Biofilms Microbiomes | 10.1038/s41522-025-00717-7 | 2025 | | |
| Modulating the developing gut microbiota with 2'-fucosyllactose and pooled human milk oligosaccharides. | Renwick S, Furst A, Knip M, DIABIMMUNE Study Group, Bode L, Danska JS, Allen-Vercoe E. | Microbiome | 10.1186/s40168-025-02034-9 | 2025 | | |
| Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children. | Lapidot Y, Reshef L, Maya M, Cohen D, Gophna U, Muhsen K. | NPJ Biofilms Microbiomes | 10.1038/s41522-022-00271-6 | 2022 | | |
| Metabolism | Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction. | Tao Z, Chen Y, He F, Tang J, Zhan L, Hu H, Ding Z, Ruan S, Chen Y, Chen B, Wang Y, Guo X, Xie L, Zhong M, Huang Q. | Microbiol Spectr | 10.1128/spectrum.00076-23 | 2023 | |
| Pathogenicity | Integrative metagenomic and metabolomic analyses reveal gut microbiota-derived multiple hits connected to development of gestational diabetes mellitus in humans. | Ye D, Huang J, Wu J, Xie K, Gao X, Yan K, Zhang P, Tao Y, Li Y, Zang S, Rong X, Li J, Guo J. | Gut Microbes | 10.1080/19490976.2022.2154552 | 2023 | |
| Dietary Protein and Fiber Affect Gut Microbiome and Treg/Th17 Commitment in Chronic Kidney Disease Mice. | Serrano M, Srivastava A, Buck G, Zhu B, Edupuganti L, Adegbulugbe E, Shankaranarayanan D, Kopp JB, Raj DS. | Am J Nephrol | 10.1159/000526957 | 2022 | | |
| Pathogenicity | Anti-Amnesic Effect of Synbiotic Supplementation Containing Corni fructus and Limosilactobacillus reuteri in DSS-Induced Colitis Mice. | Lee HL, Kim JM, Moon JH, Kim MJ, Jeong HR, Go MJ, Kim HJ, Eo HJ, Lee U, Heo HJ. | Int J Mol Sci | 10.3390/ijms24010090 | 2022 | |
| Transcriptome | The altered TBI fecal microbiome is stable and functionally distinct. | Pyles RB, Miller AL, Urban RJ, Sheffield-Moore M, Wright TJ, Maxwell CA, Randolph KM, Danesi CP, McGovern KA, Vargas J, Armstrong P, Kreber L, Cumpa G, Randall K, Morrison M, Masel BE. | Front Mol Neurosci | 10.3389/fnmol.2024.1341808 | 2024 | |
| Pathogenicity | Gut microbiota is associated with dietary intake and metabolic markers in healthy individuals. | Gaundal L, Myhrstad MCW, Rud I, Gjovaag T, Byfuglien MG, Retterstol K, Holven KB, Ulven SM, Telle-Hansen VH. | Food Nutr Res | 10.29219/fnr.v66.8580 | 2022 | |
| Metabolism | Treatment-Related Mechanisms of Tibetan Medicine Terminalia chebula (TC) Aqueous Extract Against Mouse Gastroenteritis Caused by Yak-Origin Salmonella Determined Using Intestinal Microbiome Analysis and Metabolomics. | Li D, Zhang K, Xue X, Bai Z, Yang, Qi J, Suolang S. | Animals (Basel) | 10.3390/ani15050755 | 2025 | |
| Pathogenicity | Phenotyping of Fecal Microbiota of Winnie, a Rodent Model of Spontaneous Chronic Colitis, Reveals Specific Metabolic, Genotoxic, and Pro-inflammatory Properties. | Tala A, Guerra F, Resta SC, Calcagnile M, Barca A, Tredici SM, De Donno MD, Vacca M, Liso M, Chieppa M, De Angelis M, Verri T, Bozzetti MG, Bucci C, Alifano P. | Inflammation | 10.1007/s10753-022-01706-0 | 2022 | |
| The Possible Preventative Role of Lactate- and Butyrate-Producing Bacteria in Colorectal Carcinogenesis. | Song CH, Kim N, Nam RH, Choi SI, Jang JY, Kim EH, Choi J, Choi Y, Yoon H, Lee SM, Seok YJ. | Gut Liver | 10.5009/gnl230385 | 2024 | | |
| Phylogeny | Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data. | Zhang Y, Zhong W, Liu W, Wang X, Lin G, Lin J, Fang J, Mou X, Jiang S, Huang J, Zhao W, Zheng Z. | Front Cell Infect Microbiol | 10.3389/fcimb.2024.1363276 | 2024 | |
| Genetics | Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice. | Yang J, Wang H, Lin X, Liu J, Feng Y, Bai Y, Liang H, Hu T, Wu Z, Lai J, Liu J, Zou Y, Wei S, Yan P. | mSystems | 10.1128/msystems.01366-24 | 2024 | |
| Prebiotics improve frailty status in community-dwelling older individuals in a double-blind, randomized, controlled trial. | Yang J, Hou L, Wang A, Shang L, Jia X, Xu R, Wang X. | J Clin Invest | 10.1172/jci176507 | 2024 | | |
| Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients. | Elkholy A, Avuthu N, Abdalla M, Behring M, Bajpai P, Kim HG, Header D, Abo Elwafa RA, Saed H, Embaby A, El-Nikhely N, Obuya S, Mohamed M, Badawy AA, Nawar A, Afaq F, Rogers LQ, Bae S, Shikany JM, Bateman LB, Fouad M, Saleh M, Samuel T, Varambally S, Guda C, Arafat W, Manne U. | Heliyon | 10.1016/j.heliyon.2023.e18035 | 2023 | | |
| Pathogenicity | Third-party fecal microbiota transplantation for high-risk treatment-naïve acute GVHD of the lower GI tract. | DeFilipp Z, Damania AV, Kim HT, Chang CC, El-Jawahri A, McAfee SL, Bottoms AS, Toncheva V, Smith MM, Dolaher M, Perry L, White M, Diana B, Connolly S, Dey BR, Frigault MJ, Newcomb RA, O'Donnell PV, Spitzer TR, Mansour MK, Weber D, Ajami NJ, Hohmann E, Jenq RR, Chen YB. | Blood Adv | 10.1182/bloodadvances.2024012556 | 2024 | |
| Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts. | Vinogradova E, Mukhanbetzhanov N, Nurgaziyev M, Jarmukhanov Z, Aipova R, Sailybayeva A, Bekbossynova M, Kozhakhmetov S, Kushugulova A. | mSystems | 10.1128/msystems.00585-24 | 2024 | | |
| Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review. | Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M. | Front Cell Infect Microbiol | 10.3389/fcimb.2022.804644 | 2022 | | |
| Pathogenicity | The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19. | Martin-Castano B, Diez-Echave P, Garcia-Garcia J, Hidalgo-Garcia L, Ruiz-Malagon AJ, Molina-Tijeras JA, Rodriguez-Sojo MJ, Redruello-Romero A, Martinez-Zaldivar M, Mota E, Cobo F, Diaz-Villamarin X, Alvarez-Estevez M, Garcia F, Morales-Garcia C, Merlos S, Garcia-Flores P, Colmenero-Ruiz M, Hernandez-Quero J, Nunez M, Rodriguez-Cabezas ME, Carazo A, Martin J, Moron R, Rodriguez Nogales A, Galvez J. | Elife | 10.7554/elife.95292 | 2025 | |
| Enzymology | Druggable proteins of Alistipes reveal promising antimicrobial targets against chronic intestinal inflammation. | Sohail S, Wisal A, Rana S, Abid Khan RM, Ullah A, Khan FA, Irfan M, Imran M, Carvalho PVSD, Rozental R, Shaheen F, Hassan SS. | Front Pharmacol | 10.3389/fphar.2025.1555062 | 2025 | |
| Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo. | De Bruyn F, James K, Cottenet G, Dominick M, Katja J. | Commun Biol | 10.1038/s42003-024-06628-1 | 2024 | | |
| Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains. | Koo H, Morrow CD. | PLoS One | 10.1371/journal.pone.0274633 | 2022 | | |
| HLA-Haplotypes Influence Microbiota Structure in Northwestern Mexican Schoolchildren Predisposed for Celiac Disease or Type 1 Diabetes. | Aguayo-Patron SV, Trujillo-Rivera OA, Cornejo-Granados F, Ochoa-Leyva A, Calderon de la Barca AM. | Microorganisms | 10.3390/microorganisms11061412 | 2023 | | |
| Pathogenicity | Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. | Zuo T, Liu Q, Zhang F, Lui GC, Tso EY, Yeoh YK, Chen Z, Boon SS, Chan FK, Chan PK, Ng SC. | Gut | 10.1136/gutjnl-2020-322294 | 2021 | |
| Specific network information gain for detecting the critical state of colorectal cancer based on gut microbiome. | Peng X, Gao R, Ren J, Lu J, Ma X, Li P. | Brief Bioinform | 10.1093/bib/bbad465 | 2023 | | |
| The gut microbiota and diabetic nephropathy: an observational study review and bidirectional Mendelian randomization study. | Han YZ, Wang YZY, Zhu XY, Du BX, Wang YX, Zhang XQ, Jia JM, Liu WJ, Zheng HJ. | Trials | 10.1186/s13063-025-08755-4 | 2025 | | |
| Probiotics as Adjunctive Treatment for Patients Contracted COVID-19: Current Understanding and Future Needs. | Peng J, Zhang M, Yao G, Kwok LY, Zhang W. | Front Nutr | 10.3389/fnut.2021.669808 | 2021 | | |
| Phylogeny | Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development. | Tito RY, Verbandt S, Aguirre Vazquez M, Lahti L, Verspecht C, Llorens-Rico V, Vieira-Silva S, Arts J, Falony G, Dekker E, Reumers J, Tejpar S, Raes J. | Nat Med | 10.1038/s41591-024-02963-2 | 2024 | |
| Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus. | Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K. | Sci Rep | 10.1038/s41598-024-54769-4 | 2024 | | |
| Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study. | Chen J, Wang A, Wang Q. | BMC Bioinformatics | 10.1186/s12859-021-04199-0 | 2021 | | |
| Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species. | Colosimo R, Harris HC, Ahn-Jarvis J, Troncoso-Rey P, Finnigan TJA, Wilde PJ, Warren FJ. | Commun Biol | 10.1038/s42003-024-05893-4 | 2024 | | |
| Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria. | Calvigioni M, Panattoni A, Biagini F, Donati L, Mazzantini D, Massimino M, Daddi C, Celandroni F, Vozzi G, Ghelardi E. | Microbiol Spectr | 10.1128/spectrum.00336-23 | 2023 | | |
| Gut microbiota in systemic lupus erythematosus patients and lupus mouse model: a cross species comparative analysis for biomarker discovery. | Toumi E, Goutorbe B, Plauzolles A, Bonnet M, Mezouar S, Militello M, Mege JL, Chiche L, Halfon P. | Front Immunol | 10.3389/fimmu.2022.943241 | 2022 | | |
| Pathogenicity | SARS-CoV-2-Indigenous Microbiota Nexus: Does Gut Microbiota Contribute to Inflammation and Disease Severity in COVID-19? | Chattopadhyay I, Shankar EM. | Front Cell Infect Microbiol | 10.3389/fcimb.2021.590874 | 2021 | |
| Ileocolonic Healing after Small Ileocecal Resection in Mice: NOD2 Deficiency Impairs Anastomotic Healing by Local Mechanisms. | Witte MB, Saupe J, Reiner J, Bannert K, Schafmayer C, Lamprecht G, Berlin P. | J Clin Med | 10.3390/jcm12103601 | 2023 | | |
| AhR Activation Transcriptionally Induces Anti-Microbial Peptide Alpha-Defensin 1 Leading to Reversal of Gut Microbiota Dysbiosis and Colitis. | Palrasu M, Kakar K, Marudamuthu A, Hamida H, Thada S, Zhong Y, Staley S, Busbee PB, Li J, Garcia-Buitrago M, Nagarkatti M, Nagarkatti P. | Gut Microbes | 10.1080/19490976.2025.2460538 | 2025 | | |
| Pathogenicity | Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM. | Chen Y, Lin H, Cole M, Morris A, Martinson J, Mckay H, Mimiaga M, Margolick J, Fitch A, Methe B, Srinivas VR, Peddada S, Rinaldo CR. | Microbiome | 10.1186/s40168-021-01168-w | 2021 | |
| COVID-19 and Gut Microbiota: A Potential Connection. | Rajput S, Paliwal D, Naithani M, Kothari A, Meena K, Rana S. | Indian J Clin Biochem | 10.1007/s12291-020-00948-9 | 2021 | | |
| Longitudinal phage-bacteria dynamics in the early life gut microbiome. | Tisza MJ, Lloyd RE, Hoffman K, Smith DP, Rewers M, Javornik Cregeen SJ, Petrosino JF. | Nat Microbiol | 10.1038/s41564-024-01906-4 | 2025 | | |
| Oral exposure to Staphylococcus aureus enterotoxin B could promote the Ovalbumin-induced food allergy by enhancing the activation of DCs and T cells. | Yuan J, Tong P, Meng X, Wu Y, Li X, Gao J, Chen H. | Front Immunol | 10.3389/fimmu.2023.1250458 | 2023 | | |
| Genetics | Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities. | Mobegi FM, Leong LE, Thompson F, Taylor SM, Harriss LR, Choo JM, Taylor SL, Wesselingh SL, McDermott R, Ivey KL, Rogers GB. | Elife | 10.7554/elife.58407 | 2020 | |
| Genetics | Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in (hAbeta-KI) mice. | Dunham SJB, Avelar-Barragan J, Rothman JA, Adams ED, Faraci G, Forner S, Kawauchi S, Tenner AJ, Green KN, LaFerla FM, MacGregor GR, Mapstone M, Whiteson KL. | Alzheimers Dement | 10.1002/alz.13794 | 2024 | |
| Pathogenicity | Alterations of the Gut Microbiota in Multiple System Atrophy Patients. | Wan L, Zhou X, Wang C, Chen Z, Peng H, Hou X, Peng Y, Wang P, Li T, Yuan H, Shi Y, Hou X, Xu K, Xie Y, He L, Xia K, Tang B, Jiang H. | Front Neurosci | 10.3389/fnins.2019.01102 | 2019 | |
| Pathogenicity | A Six-Day, Lifestyle-Based Immersion Program Mitigates Cardiovascular Risk Factors and Induces Shifts in Gut Microbiota, Specifically Lachnospiraceae, Ruminococcaceae, Faecalibacterium prausnitzii: A Pilot Study. | Ahrens AP, Culpepper T, Saldivar B, Anton S, Stoll S, Handberg EM, Xu K, Pepine C, Triplett EW, Aggarwal M. | Nutrients | 10.3390/nu13103459 | 2021 | |
| Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China. | Yang Y, Chen J, Gao H, Cui M, Zhu M, Xiang X, Wang Q. | Front Cell Infect Microbiol | 10.3389/fcimb.2024.1374544 | 2024 | | |
| Genetics | Effect of minocycline, methyl prednisolone, or combination treatment on the colonic bacterial population in a state of colonic inflammation using the murine dextran sulfate sodium model. | Khajah MA, Hawai S. | Microb Cell Fact | 10.1186/s12934-023-02242-8 | 2023 | |
| Gut microbiota, angiotensin-converting enzyme, celiac disease, and risk of COVID-19 infection: a review. | Gholam-Mostafaei FS, Didari T, Ramandi M, Vafaee R, Rostami-Nejad M. | Gastroenterol Hepatol Bed Bench | 2021 | | ||
| Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions. | Gnanasekaran T, Sarathi A, Fang Q, Azarm A, Assis Geraldo J, Nigro E, Arumugam M. | mSystems | 10.1128/msystems.01249-22 | 2023 | | |
| Pathogenicity | Disease severity and proton pump inhibitor use impact strongest on faecal microbiome composition in liver cirrhosis. | Stadlbauer V, Komarova I, Klymiuk I, Durdevic M, Reisinger A, Blesl A, Rainer F, Horvath A. | Liver Int | 10.1111/liv.14382 | 2020 | |
| Oral and gut dysbiosis leads to functional alterations in Parkinson's disease. | Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW, Chung SJ. | NPJ Parkinsons Dis | 10.1038/s41531-022-00351-6 | 2022 | | |
| Consistent signatures in the human gut microbiome of longevous populations. | Chen S, Zhang Z, Liu S, Chen T, Lu Z, Zhao W, Mou X, Liu S. | Gut Microbes | 10.1080/19490976.2024.2393756 | 2024 | | |
| The intestinal microbiome of inflammatory bowel disease across the pediatric age range. | Conrad MA, Bittinger K, Ren Y, Kachelries K, Vales J, Li H, Wu GD, Bushman FD, Devoto M, Baldassano RN, Kelsen JR. | Gut Microbes | 10.1080/19490976.2024.2317932 | 2024 | | |
| Genetics | Gut Microbial Genes and Metabolism for Methionine and Branched-Chain Amino Acids in Diabetic Nephropathy. | Kim JE, Nam H, Park JI, Cho H, Lee J, Kim HE, Kim DK, Joo KW, Kim YS, Kim BS, Park S, Lee H. | Microbiol Spectr | 10.1128/spectrum.02344-22 | 2023 | |
| Pathogenicity | Gut Microbiota Characteristics of People with Obesity by Meta-Analysis of Existing Datasets. | Gong J, Shen Y, Zhang H, Cao M, Guo M, He J, Zhang B, Xiao C. | Nutrients | 10.3390/nu14142993 | 2022 | |
| A Scoping Review of Gut Microbiome and Bifidobacterium Research in Zimbabwe: Implications for Future Studies. | Zhou DT, Mudhluli TE, Hall LJ, Manasa J, Munyati S. | Pediatric Health Med Ther | 10.2147/phmt.s414766 | 2023 | | |
| Alterations in Gut Microbiota Composition in Patients with COVID-19: A Pilot Study of Whole Hypervariable 16S rRNA Gene Sequencing. | Mankowska-Wierzbicka D, Zuraszek J, Wierzbicka A, Gabryel M, Mahadea D, Baturo A, Zakerska-Banaszak O, Slomski R, Skrzypczak-Zielinska M, Dobrowolska A. | Biomedicines | 10.3390/biomedicines11020367 | 2023 | | |
| A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes | Chen M, Peng Y, Hu Y, Kang Z, Chen T, Zhang Y, Chen X, Li Q, Yuan Z, Wu Y, Xu H, Zhou G, Liu T, Zhou H, Yuan C, Huang W, Zhang W. | Acta pharmaceutica Sinica. B | 2025 | | ||
| The gut microbiome affects response of treatments in HER2-negative advanced gastric cancer. | Han Z, Cheng S, Dai D, Kou Y, Zhang X, Li F, Yin X, Ji J, Zhang Z, Wang X, Zhu N, Zhang Q, Tan Y, Guo X, Shen L, Peng Z. | Clin Transl Med | 10.1002/ctm2.1312 | 2023 | | |
| Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities. | Alessandri G, Rizzo SM, Mancabelli L, Fontana F, Longhi G, Turroni F, van Sinderen D, Ventura M. | Microb Biotechnol | 10.1111/1751-7915.14509 | 2024 | | |
| Dietary intervention with functional foods modulating gut microbiota for improving the efficacy of COVID-19 vaccines. | Oh S, Seo H. | Heliyon | 10.1016/j.heliyon.2023.e15668 | 2023 | | |
| The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection. | Piazzesi A, Pane S, Del Chierico F, Romani L, Campana A, Palma P, Putignani L. | Front Cell Infect Microbiol | 10.3389/fcimb.2024.1335450 | 2024 | | |
| Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples. | Pietila S, Suomi T, Elo LL. | ISME Commun | 10.1038/s43705-022-00137-0 | 2022 | | |
| A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers. | Xu J, Zheng Z, Yang L, Li R, Ma X, Zhang J, Yin F, Liu L, Xu Q, Shen Q, Shen X, Wu C, Liu J, Qin N, Sheng J, Jin P, Jin P. | Cell Biosci | 10.1186/s13578-022-00940-1 | 2022 | | |
| Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer. | Wu X, Tang Z, Zhao R, Wang Y, Wang X, Liu S, Zou H. | Front Oncol | 10.3389/fonc.2023.1218056 | 2023 | | |
| Detection of Intestinal Dysbiosis in Post-COVID-19 Patients One to Eight Months after Acute Disease Resolution. | Ferreira-Junior AS, Borgonovi TF, De Salis LVV, Leite AZ, Dantas AS, De Salis GVV, Cruz GNF, De Oliveira LFV, Gomes E, Penna ALB, De Oliveira GLV. | Int J Environ Res Public Health | 10.3390/ijerph191610189 | 2022 | | |
| Sugar lowering in fermented apple-pear juice orchestrates a promising metabolic answer in the gut microbiome and intestinal integrity. | Tlais AZA, Polo A, Granehall L, Filannino P, Vincentini O, De Battistis F, Di Cagno R, Gobbetti M. | Curr Res Food Sci | 10.1016/j.crfs.2024.100833 | 2024 | | |
| Our experience with 80 cases of SARS-CoV-2-Clostridioides difficile co-infection: An observational study. | Birlutiu V, Dobritoiu ES, Lupu CD, Herteliu C, Birlutiu RM, Dragomirescu D, Vorovenci A. | Medicine (Baltimore) | 10.1097/md.0000000000029823 | 2022 | | |
| Gastrointestinal symptoms in patients with coronavirus disease 2019 (COVID-19) - friend or foe? | Lewandowski K, Kaniewska M, Rosolowski M, Tworek A, Rydzewska G. | Prz Gastroenterol | 10.5114/pg.2021.111000 | 2022 | | |
| Gut metagenome-derived signature predicts hepatic decompensation and mortality in NAFLD-related cirrhosis. | Sharpton SR, Oh TG, Madamba E, Wang C, Yu RT, Atkins AR, Huan T, Downes M, Evans RM, Loomba R. | Aliment Pharmacol Ther | 10.1111/apt.17236 | 2022 | | |
| Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis. | Dahal RH, Kim S, Kim YK, Kim ES, Kim J. | Front Microbiol | 10.3389/fmicb.2023.1174832 | 2023 | | |
| Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1. | Petersen AO, Jokinen M, Plichta DR, Liebisch G, Gronwald W, Dettmer K, Oefner PJ, Vlamakis H, Chung DC, Ranki A, Xavier RJ. | J Allergy Clin Immunol | 10.1016/j.jaci.2021.03.025 | 2021 | | |
| Genetics | Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools. | Derakhshani H, Bernier SP, Marko VA, Surette MG. | BMC Genomics | 10.1186/s12864-020-06910-6 | 2020 | |
| Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity. | Maeda Y, Motooka D, Kawasaki T, Oki H, Noda Y, Adachi Y, Niitsu T, Okamoto S, Tanaka K, Fukushima K, Amiya S, Hara R, Oguro-Igashira E, Matsuki T, Hirata H, Takeda Y, Kida H, Kumanogoh A, Nakamura S, Takeda K. | BMC Infect Dis | 10.1186/s12879-022-07358-7 | 2022 | | |
| Genetics | Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes. | Obon-Santacana M, Mas-Lloret J, Bars-Cortina D, Criado-Mesas L, Carreras-Torres R, Diez-Villanueva A, Moratalla-Navarro F, Guino E, Ibanez-Sanz G, Rodriguez-Alonso L, Mulet-Margalef N, Mata A, Garcia-Rodriguez A, Duell EJ, Pimenoff VN, Moreno V. | Cancers (Basel) | 10.3390/cancers14174214 | 2022 | |
| Genetics | Quercetin positively affects gene expression profiles and metabolic pathway of antibiotic-treated mouse gut microbiota. | Mi W, Hu Z, Xu L, Bian X, Lian W, Yin S, Zhao S, Gao W, Guo C, Shi T. | Front Microbiol | 10.3389/fmicb.2022.983358 | 2022 | |
| Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer. | Avuthu N, Guda C. | Microbiol Spectr | 10.1128/spectrum.00013-22 | 2022 | | |
| Effects of the Lipid Profile, Type 2 Diabetes and Medication on the Metabolic Syndrome-Associated Gut Microbiome. | Gradisteanu Pircalabioru G, Liaw J, Gundogdu O, Corcionivoschi N, Ilie I, Oprea L, Musat M, Chifiriuc MC. | Int J Mol Sci | 10.3390/ijms23147509 | 2022 | | |
| Featured Gut Microbiomes Associated With the Progression of Chronic Hepatitis B Disease. | Chen Z, Xie Y, Zhou F, Zhang B, Wu J, Yang L, Xu S, Stedtfeld R, Chen Q, Liu J, Zhang X, Xu H, Ren J. | Front Microbiol | 10.3389/fmicb.2020.00383 | 2020 | | |
| Genetics | When old metagenomic data meet newly sequenced genomes, a case study. | Li X, Naser SA, Khaled A, Hu H, Li X. | PLoS One | 10.1371/journal.pone.0198773 | 2018 | |
| The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health. | Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A. | Front Immunol | 10.3389/fimmu.2020.00906 | 2020 | | |
| Impact of cigarette smoking on gut microbial dysbiosis: a structured literature review. | Imade EE, Obayagbona NO. | Gut Microbiome (Camb) | 10.1017/gmb.2024.3 | 2024 | | |
| Gut microbiome functionality might be associated with exercise tolerance and recurrence of resected early-stage lung cancer patients. | Marfil-Sanchez A, Seelbinder B, Ni Y, Varga J, Berta J, Hollosi V, Dome B, Megyesfalvi Z, Dulka E, Galffy G, Weiss GJ, Panagiotou G, Lohinai Z. | PLoS One | 10.1371/journal.pone.0259898 | 2021 | | |
| Pathogenicity | Perturbation of the human gastrointestinal tract microbial ecosystem by oral drugs to treat chronic disease results in a spectrum of individual specific patterns of extinction and persistence of dominant microbial strains. | Koo H, Morrow CD. | PLoS One | 10.1371/journal.pone.0242021 | 2020 | |
| Genetics | HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data. | Hiseni P, Rudi K, Wilson RC, Hegge FT, Snipen L. | Microbiome | 10.1186/s40168-021-01114-w | 2021 | |
| Pathogenicity | Altered Gut Microbial Profile Accompanied by Abnormal Fatty Acid Metabolism Activity Exacerbates Endometrial Cancer Progression. | Zhao SS, Chen L, Yang J, Wu ZH, Wang XY, Zhang Q, Liu WJ, Liu HX. | Microbiol Spectr | 10.1128/spectrum.02612-22 | 2022 | |
| Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity. | Hazan S, Stollman N, Bozkurt HS, Dave S, Papoutsis AJ, Daniels J, Barrows BD, Quigley EM, Borody TJ. | BMJ Open Gastroenterol | 10.1136/bmjgast-2022-000871 | 2022 | | |
| Pathogenicity | Role of the Microbiome in the Pathogenesis of COVID-19. | De R, Dutta S. | Front Cell Infect Microbiol | 10.3389/fcimb.2022.736397 | 2022 | |
| Metabolism | Bacteroidales recruit IL-6-producing intraepithelial lymphocytes in the colon to promote barrier integrity. | Kuhn KA, Schulz HM, Regner EH, Severs EL, Hendrickson JD, Mehta G, Whitney AK, Ir D, Ohri N, Robertson CE, Frank DN, Campbell EL, Colgan SP. | Mucosal Immunol | 10.1038/mi.2017.55 | 2018 | |
| The primate gut mycobiome-bacteriome interface is impacted by environmental and subsistence factors. | Sharma AK, Davison S, Pafco B, Clayton JB, Rothman JM, McLennan MR, Cibot M, Fuh T, Vodicka R, Robinson CJ, Petrzelkova K, Gomez A. | NPJ Biofilms Microbiomes | 10.1038/s41522-022-00274-3 | 2022 | | |
| Pathogenicity | Antimicrobial Susceptibility Patterns of Anaerobic Bacterial Clinical Isolates From 2014 to 2016, Including Recently Named or Renamed Species. | Byun JH, Kim M, Lee Y, Lee K, Chong Y. | Ann Lab Med | 10.3343/alm.2019.39.2.190 | 2019 | |
| Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients. | Sun Z, Song ZG, Liu C, Tan S, Lin S, Zhu J, Dai FH, Gao J, She JL, Mei Z, Lou T, Zheng JJ, Liu Y, He J, Zheng Y, Ding C, Qian F, Zheng Y, Chen YM. | BMC Med | 10.1186/s12916-021-02212-0 | 2022 | | |
| Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria. | Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S, Buhl EM, Abt B, Neuhaus K, Velge P, Overmann J, Kaspers B, Clavel T. | mSystems | 10.1128/msystems.01300-20 | 2021 | | |
| Gut Microbiota Status in COVID-19: An Unrecognized Player? | Donati Zeppa S, Agostini D, Piccoli G, Stocchi V, Sestili P. | Front Cell Infect Microbiol | 10.3389/fcimb.2020.576551 | 2020 | | |
| Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects. | Benitez-Paez A, Hartstra AV, Nieuwdorp M, Sanz Y. | Gut Microbes | 10.1080/19490976.2022.2078621 | 2022 | | |
| Regulatory Effects of Combined Dietary Supplementation With Essential Oils and Organic Acids on Microbial Communities of Cobb Broilers. | Qiao J, Shang Z, Liu X, Wang K, Wu Z, Wei Q, Li H. | Front Microbiol | 10.3389/fmicb.2021.814626 | 2021 | | |
| Genetics | Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates. | Bosak J, Lexa M, Fiedorova K, Gadara DC, Micenkova L, Spacil Z, Litzman J, Freiberger T, Smajs D. | Front Immunol | 10.3389/fimmu.2021.671239 | 2021 | |
| Metabolism | Microbiota-derived short-chain fatty acids do not interfere with SARS-CoV-2 infection of human colonic samples. | Pascoal LB, Rodrigues PB, Genaro LM, Gomes ABDSP, Toledo-Teixeira DA, Parise PL, Bispo-Dos-Santos K, Simeoni CL, Guimaraes PV, Buscaratti LI, Elston JGA, Marques-Souza H, Martins-de-Souza D, Ayrizono MLS, Velloso LA, Proenca-Modena JL, Moraes-Vieira PMM, Mori MAS, Farias AS, Vinolo MAR, Leal RF. | Gut Microbes | 10.1080/19490976.2021.1874740 | 2021 | |
| The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps. | Hanes D, Nowinski B, Lamb JJ, Larson IA, McDonald D, Knight R, Song SJ, Patno N. | Front Nutr | 10.3389/fnut.2022.987216 | 2022 | | |
| Genetics | How genomics can be used to understand host susceptibility to enteric infection, aiding in the development of vaccines and immunotherapeutic interventions. | Mottram L, Chakraborty S, Cox E, Fleckenstein J. | Vaccine | 10.1016/j.vaccine.2019.01.016 | 2019 | |
| Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy. | Thomas AM, Fidelle M, Routy B, Kroemer G, Wargo JA, Segata N, Zitvogel L. | Nat Rev Clin Oncol | 10.1038/s41571-023-00785-8 | 2023 | | |
| Effects of Fecal Microbiome Transfer in Adolescents With Obesity: The Gut Bugs Randomized Controlled Trial. | Leong KSW, Jayasinghe TN, Wilson BC, Derraik JGB, Albert BB, Chiavaroli V, Svirskis DM, Beck KL, Conlon CA, Jiang Y, Schierding W, Vatanen T, Holland DJ, O'Sullivan JM, Cutfield WS. | JAMA Netw Open | 10.1001/jamanetworkopen.2020.30415 | 2020 | | |
| Genetics | Relationship between the Gut Microbiome and Energy/Nutrient Intake in a Confined Bioregenerative Life Support System. | Chen J, Wang Q, Hao Z, Li Z, Sahu SK, Liu H, Xiao L. | Appl Environ Microbiol | 10.1128/aem.02465-19 | 2020 | |
| A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. | Zeng S, Patangia D, Almeida A, Zhou Z, Mu D, Paul Ross R, Stanton C, Wang S. | Nat Commun | 10.1038/s41467-022-32805-z | 2022 | | |
| Pathogenicity | Microbiota Modulation of the Gut-Lung Axis in COVID-19. | de Oliveira GLV, Oliveira CNS, Pinzan CF, de Salis LVV, Cardoso CRB. | Front Immunol | 10.3389/fimmu.2021.635471 | 2021 | |
| Intestinal dysbiosis exacerbates the pathogenesis of psoriasis-like phenotype through changes in fatty acid metabolism. | Zhao Q, Yu J, Zhou H, Wang X, Zhang C, Hu J, Hu Y, Zheng H, Zeng F, Yue C, Gu L, Wang Z, Zhao F, Zhou P, Zhang H, Huang N, Wu W, Zhou Y, Li J, Li J. | Signal Transduct Target Ther | 10.1038/s41392-022-01219-0 | 2023 | | |
| Genetics | Variation and transmission of the human gut microbiota across multiple familial generations. | Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. | Nat Microbiol | 10.1038/s41564-021-01021-8 | 2022 | |
| Metabolism | Isolation of Anti-Inflammatory and Epithelium Reinforcing Bacteroides and Parabacteroides Spp. from A Healthy Fecal Donor. | Hiippala K, Kainulainen V, Suutarinen M, Heini T, Bowers JR, Jasso-Selles D, Lemmer D, Valentine M, Barnes R, Engelthaler DM, Satokari R. | Nutrients | 10.3390/nu12040935 | 2020 | |
| Genetics | Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. | Ravi A, Halstead FD, Bamford A, Casey A, Thomson NM, van Schaik W, Snelson C, Goulden R, Foster-Nyarko E, Savva GM, Whitehouse T, Pallen MJ, Oppenheim BA. | Microb Genom | 10.1099/mgen.0.000293 | 2019 | |
| The Role of the Microbiome on the Pathogenesis and Treatment of Colorectal Cancer. | Yu I, Wu R, Tokumaru Y, Terracina KP, Takabe K. | Cancers (Basel) | 10.3390/cancers14225685 | 2022 | | |
| Hypergravity disrupts murine intestinal microbiota. | Alauzet C, Cunat L, Wack M, Lozniewski A, Busby H, Agrinier N, Cailliez-Grimal C, Frippiat JP. | Sci Rep | 10.1038/s41598-019-45153-8 | 2019 | | |
| Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization. | Zuo T, Zhang F, Lui GCY, Yeoh YK, Li AYL, Zhan H, Wan Y, Chung ACK, Cheung CP, Chen N, Lai CKC, Chen Z, Tso EYK, Fung KSC, Chan V, Ling L, Joynt G, Hui DSC, Chan FKL, Chan PKS, Ng SC. | Gastroenterology | 10.1053/j.gastro.2020.05.048 | 2020 | | |
| Proteome | Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. | Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Tolic N, Sachsenberg T, McCalder J, Lipton MS, Strous M. | Microbiome | 10.1186/s40168-022-01454-1 | 2023 | |
| Enzymology | Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet. | Roager HM, Licht TR, Poulsen SK, Larsen TM, Bahl MI. | Appl Environ Microbiol | 10.1128/aem.03549-13 | 2014 | |
| Phylogeny | Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models. | Jiang P, Wu S, Luo Q, Zhao XM, Chen WH, Chen WH. | mSystems | 10.1128/msystems.00112-21 | 2021 | |
| Pathogenicity | Probiotic-directed modulation of gut microbiota is basal microbiome dependent. | Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee YK, Zhang H. | Gut Microbes | 10.1080/19490976.2020.1736974 | 2020 | |
| Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation. | Bourke CD, Gough EK, Pimundu G, Shonhai A, Berejena C, Terry L, Baumard L, Choudhry N, Karmali Y, Bwakura-Dangarembizi M, Musiime V, Lutaakome J, Kekitiinwa A, Mutasa K, Szubert AJ, Spyer MJ, Deayton JR, Glass M, Geum HM, Pardieu C, Gibb DM, Klein N, Edens TJ, Walker AS, Manges AR, Prendergast AJ. | Sci Transl Med | 10.1126/scitranslmed.aav0537 | 2019 | | |
| Bacteroidota and Lachnospiraceae integration into the gut microbiome at key time points in early life are linked to infant neurodevelopment. | Oliphant K, Ali M, D'Souza M, Hughes PD, Sulakhe D, Wang AZ, Xie B, Yeasin R, Msall ME, Andrews B, Claud EC. | Gut Microbes | 10.1080/19490976.2021.1997560 | 2021 | | |
| Pathogenicity | Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. | Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC. | BMC Genomics | 10.1186/s12864-016-2777-0 | 2016 | |
| Genetics | Selective colonization ability of human fecal microbes in different mouse gut environments. | Zhou W, Chow KH, Fleming E, Oh J. | ISME J | 10.1038/s41396-018-0312-9 | 2019 | |
| The Role of Dysbiosis in Critically Ill Patients With COVID-19 and Acute Respiratory Distress Syndrome. | Battaglini D, Robba C, Fedele A, Tranca S, Sukkar SG, Di Pilato V, Bassetti M, Giacobbe DR, Vena A, Patroniti N, Ball L, Brunetti I, Torres Marti A, Rocco PRM, Pelosi P. | Front Med (Lausanne) | 10.3389/fmed.2021.671714 | 2021 | | |
| Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle. | Reti KL, Thomas MC, Yanke LJ, Selinger LB, Inglis GD. | Gut Pathog | 10.1186/1757-4749-5-8 | 2013 | | |
| The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens. | Wetzels SU, Eger M, Burmester M, Kreienbrock L, Abdulmawjood A, Pinior B, Wagner M, Breves G, Mann E. | PLoS One | 10.1371/journal.pone.0192256 | 2018 | | |
| Phylogeny | Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov. | Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003778 | 2020 | |
| Phylogeny | Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin. | Song Y, Kononen E, Rautio M, Liu C, Bryk A, Eerola E, Finegold SM | Int J Syst Evol Microbiol | 10.1099/ijs.0.64318-0 | 2006 | |
How to citeIf you want to cite this particular strain cite the following doi:
https://doi.org/10.13145/bacdive14031.20260601.11
When using BacDive for research please cite the following paper
BacDive in 2025: the core database for prokaryotic strain data
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