(stanton, catherine[Author] OR o'toole, paul[Author] OR cotter, paul[Author] OR theile, ines[Author] OR arendt, elke[Author] OR o'sullivan, orla[Author] OR walter, jens[Author] OR dempsey, eugene[Author] OR mcauliffe, fionnula[Author] OR o'mahony, se - Search Results

Year	Number of Results
2004	2
2005	5
2006	3
2007	5
2008	5
2009	7
2010	9
2011	7
2012	12
2013	16
2014	26
2015	43
2016	46
2017	62
2018	71
2019	84
2020	112
2021	114
2022	111
2023	91
2024	108
2025	78
2026	32

1

The effects of a powdered meal replacement intake on inflammation, gut microbiota, and metabolism compared to habitual diet in people with excess body weight - results from a randomized controlled trial.

Montenegro J, Oliveira CLP, Nguyen NK, Armet AM, Berg A, Sharma AM, Mereu L, Cominetti C, Ghosh S, Cani PD, Richard C, Walter J, Prado CM. Montenegro J, et al. Among authors: walter j. J Nutr. 2026 May 15:101595. doi: 10.1016/j.tjnut.2026.101595. Online ahead of print. J Nutr. 2026. PMID: 42142662

2

Characterizing microbiomes of African fermented foods in a global context.

Leech J, Obafemi YD, Breselge S, Aremu T, Obadina AO, Itohan ME, Ezekiel CN, Parkouda C, Tankoano A, Traoré K, Banwo K, Kunadu AP, Madilo FK, Sanni AI, Ogunremi OR, Onipede G, Odeny DA, Otieno C, Claesson MJ, Cotter PD. Leech J, et al. Among authors: cotter pd. Microbiology (Reading). 2026 May;172(5):001695. doi: 10.1099/mic.0.001695. Microbiology (Reading). 2026. PMID: 42084497 Free PMC article.

3

The Gut in Early Life-Postnatal Challenges.

Benninga MA, Schäfer KH, Piloquet H, Stanton C. Benninga MA, et al. Among authors: stanton c. Children (Basel). 2026 Mar 30;13(4):480. doi: 10.3390/children13040480. Children (Basel). 2026. PMID: 42073058 Free PMC article. Review.

4

Breath volatilome analysis reveals new gut microbiome-related metabolites that discriminate high versus low dietary fibre intake.

Autuori M, Neyrinck AM, Lengelé L, Olivera EV, Rombaux M, Rodriguez J, Cani PD, Walter J, Bindels LB, Delzenne NM. Autuori M, et al. Among authors: walter j. Clin Nutr. 2026 Apr 14;61:106662. doi: 10.1016/j.clnu.2026.106662. Online ahead of print. Clin Nutr. 2026. PMID: 42054964 Free article.

5

Unmelted, melted, and deconstructed Cheddar cheese: effects on the gut microbiome from a human dietary intervention study.

Chonnacháin CN, Gibney ER, Feeney EL, Rooney M, O'Connor A, Noronha N, Crispie F, Cotter PD, FitzGerald JA. Chonnacháin CN, et al. Among authors: cotter pd. Front Microbiol. 2026 Apr 10;17:1702111. doi: 10.3389/fmicb.2026.1702111. eCollection 2026. Front Microbiol. 2026. PMID: 42039839 Free PMC article.

6

Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns.

Goswami S, Ansari A, Saraf C, O'Toole PW, Shanahan F, Ahuja V, Ghosh TS. Goswami S, et al. Among authors: o toole pw. Nat Commun. 2026 Apr 23. doi: 10.1038/s41467-026-72289-9. Online ahead of print. Nat Commun. 2026. PMID: 42020446 Free article.

7

Investigating the role of bacterial raw milk community members in chlorate reduction.

Srinivas M, O'Sullivan O, Cotter PD, van Sinderen D, Kenny JG. Srinivas M, et al. Among authors: kenny jg, o sullivan o, cotter pd. Access Microbiol. 2026 Apr 20;8(4):001088.v3. doi: 10.1099/acmi.0.001088.v3. eCollection 2026. Access Microbiol. 2026. PMID: 42016597 Free PMC article.

8

Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.

Khan A, Breselge S, O'Mahony AK, O'Sullivan O, Cotter PD, McCarthy SN, Mahony J, Kenny JG. Khan A, et al. Among authors: kenny jg, o sullivan o, cotter pd. NPJ Biofilms Microbiomes. 2026 Apr 15. doi: 10.1038/s41522-026-00985-x. Online ahead of print. NPJ Biofilms Microbiomes. 2026. PMID: 41986376 Free article. Review.

9

The gut microbiota of hepato-pancreatico-biliary and gastric cancer patients is altered in composition and functionality.

Daly L, Sullivan ES, Fouhy F, Watkins C, Linaries D, Power D, O'Suilleabhain C, O'Sullivan A, O'Toole P, Ross P, Stanton C, Ryan A. Daly L, et al. Among authors: o toole p, stanton c. Ir J Med Sci. 2026 Apr 10. doi: 10.1007/s11845-025-04166-1. Online ahead of print. Ir J Med Sci. 2026. PMID: 41961453 No abstract available.

10

Infant gut microbiomes contribute to metabolic states that impact brain function.

Midani FS, Lee DH, Moon Y, Seale M, Horvath TD, Ardis AK, Cantú J, Coles E, Pizzini JD, Zhu D, Dooling SW, Ahern GJ, Ardis CK, Beckford A, Ruggiero NM, Shin J, Joos R, Stanton C, Ross RP, Dai DLY, Mandhane PJ, Petersen C, Turvey SE, Kiely ME, Murray DM, Costa-Mattioli M, Tolias KF, Britton RA, Danhof HA. Midani FS, et al. Among authors: stanton c. bioRxiv [Preprint]. 2026 Mar 10:2026.03.09.710596. doi: 10.64898/2026.03.09.710596. bioRxiv. 2026. PMID: 41959053 Free PMC article. Preprint.

11

Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters.

Ramakrishnan M, Cross TL, Organski AC, Saiprasad SM, Simpson AMR, Tancredi DJ, Van Haute MJ, Christensen CM, Lewis ZT, Auchtung TA, Walter J, Hutkins R, Savaiano DA. Ramakrishnan M, et al. Among authors: walter j. Gut Microbes Rep. 2025 Jun 4;2(1):2508199. doi: 10.1080/29933935.2025.2508199. eCollection 2025. Gut Microbes Rep. 2025. PMID: 41909904 Free PMC article.

12

Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.

Walsh LH, Soni V, Ancla J, Somerville V, Segata N, Joyce S, Sinderen DV, Mahony J, Shkoporov AN, Kenny JG, Cotter PD, O'Sullivan O. Walsh LH, et al. Among authors: kenny jg, o sullivan o, cotter pd. NPJ Biofilms Microbiomes. 2026 Mar 27. doi: 10.1038/s41522-026-00941-9. Online ahead of print. NPJ Biofilms Microbiomes. 2026. PMID: 41896556 Free article.

13

Avoidant/Restrictive Food Intake Disorder in Disorders of Gut-Brain Interaction: Adaptive Restriction or Psychopathology?

Li J, Das A, Quigley EMM, O'toole PW. Li J, et al. Among authors: o toole pw. Gastroenterology. 2026 Mar 25:S0016-5085(26)00247-7. doi: 10.1053/j.gastro.2025.10.297. Online ahead of print. Gastroenterology. 2026. PMID: 41895383 No abstract available.

14

Metabolic pathway analysis reveals hierarchical pentose sugar utilization and metabolic flexibility of Bifidobacterium longum.

Friess L, McAuliffe FM, Cotter PD, Shiver AL, Huang KC, de Jong A, van Sinderen D. Friess L, et al. Among authors: cotter pd. Gut Microbes. 2026 Dec 31;18(1):2647591. doi: 10.1080/19490976.2026.2647591. Epub 2026 Mar 23. Gut Microbes. 2026. PMID: 41872067 Free PMC article.

15

Plant-based proteins as functional egg replacers in pound cake: A comparative study of legume and oat ingredients.

Halm J, Nyhan L, Zannini E, Arendt EK. Halm J, et al. Among authors: arendt ek. Curr Res Food Sci. 2026 Mar 11;12:101373. doi: 10.1016/j.crfs.2026.101373. eCollection 2026. Curr Res Food Sci. 2026. PMID: 41852944 Free PMC article.

16

Comprehensive nutritional analysis of 95 oat cultivars reveals large variability in nutritional profile: protein, starch, fat, β-glucan and fibre.

Lampoglou N, Rahman A, Mullins E, Sahin AW, McCabe C, Arendt E, Brodkorb A, Freitas D. Lampoglou N, et al. Among authors: arendt e. NPJ Sci Food. 2026 Mar 17;10(1):145. doi: 10.1038/s41538-026-00800-z. NPJ Sci Food. 2026. PMID: 41844628 Free PMC article.

17

Proposal of Limosilactobacillus secundus sp. nov., Limosilactobacillus reuteri subsp. pararodentium subsp. nov., Limosilactobacillus reuteri subsp. peregrinus subsp. nov. and Limosilactobacillus reuteri subsp. simiae subsp. nov., isolated from the gastrointestinal tract of vertebrate hosts.

Guo X, Yang Y, Zhang JS, Zhang P, Walter J, Gänzle MG, Li F. Guo X, et al. Among authors: walter j. Int J Syst Evol Microbiol. 2026 Mar;76(3):007099. doi: 10.1099/ijsem.0.007099. Int J Syst Evol Microbiol. 2026. PMID: 41790565 Free PMC article.

18

Bifidobacterium breve CCFM1078 alleviates DNFB-induced atopic dermatitis in early-life via AhR activation, Th1/Th2 immune modulation, and gut microbiota regulation.

Li Y, Li H, Zhang Q, Cui S, Zhai Q, Stanton C, Ross P, Zhao J, Chen W, Yang B. Li Y, et al. Among authors: stanton c. Food Funct. 2026 Mar 23;17(6):2927-2941. doi: 10.1039/d5fo05688h. Food Funct. 2026. PMID: 41790046

19

Techno-functional and nutritional evaluation of Solein single-cell protein and its application in non-dairy yoghurt alternatives.

Caliskan C, Nyhan L, Hernández-Olivas E, Feng S, Zannini E, Sozer N, Brodkorb A, Arendt EK. Caliskan C, et al. Among authors: arendt ek. Food Res Int. 2026 Apr 1;229:118467. doi: 10.1016/j.foodres.2026.118467. Epub 2026 Jan 20. Food Res Int. 2026. PMID: 41763789 Free article.

20

Bifidobacterium longum and prebiotic interventions restore early-life high-fat/high-sugar diet-induced alterations in feeding behavior in adult mice.

Cuesta-Marti C, Ponce-España E, Uhlig F, Stoltenborg I, Wasiewska LA, Kareem L, Hedayatpour D, Olavarría-Ramírez L, Rosell-Cardona C, Bastiaanssen TFS, Tofani GSS, Valderrama B, Vlckova K, Dickson SL, Lavelle A, Stanton C, Ross RP, Cryan JF, Dinan TG, Clarke G, O'Mahony SM, Schellekens H. Cuesta-Marti C, et al. Among authors: stanton c. Nat Commun. 2026 Feb 24;17(1):1653. doi: 10.1038/s41467-026-68968-2. Nat Commun. 2026. PMID: 41735265 Free PMC article.

21

Orchestrating life's first community: molecular assembly by human milk oligosaccharides.

Zhou Y, Yang B, Zhao J, Ross P, Stanton C, Chen W. Zhou Y, et al. Among authors: stanton c. Gut Microbes. 2026 Dec 31;18(1):2632973. doi: 10.1080/19490976.2026.2632973. Epub 2026 Feb 19. Gut Microbes. 2026. PMID: 41715897 Free PMC article. Review.

22

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health.

Marco ML, Cunningham M, Bischoff SC, Clarke G, Delzenne N, Lewis JD, Meisel M, Merenstein D, O'Toole PW, Staudacher HM, Szajewska H, Wells JM, Quigley EMM. Marco ML, et al. Among authors: o toole pw. Nat Rev Gastroenterol Hepatol. 2026 May;23(5):432-448. doi: 10.1038/s41575-026-01176-x. Epub 2026 Feb 18. Nat Rev Gastroenterol Hepatol. 2026. PMID: 41709019 Review.

23

A comparative study of human milk oligosaccharides: 6'-sialyllactose enhances gut barrier function and immune homeostasis to alleviate food allergy.

Wu S, Chen H, Zhao J, Jiang S, Stanton C, Ross RP, Chen W, Yang B. Wu S, et al. Among authors: stanton c. Food Funct. 2026 Mar 9;17(5):2252-2266. doi: 10.1039/d5fo04181c. Food Funct. 2026. PMID: 41685406

24

Soy and the gut microbiome: a bi-directional relationship shaping nutrition and health.

Nolan L, O'Toole PW. Nolan L, et al. Among authors: o toole pw. Eur J Nutr. 2026 Feb 12;65(2):53. doi: 10.1007/s00394-026-03900-4. Eur J Nutr. 2026. PMID: 41677879 Free PMC article. Review.

25

Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties.

Zhang E, Claesson MJ, Cotter PD. Zhang E, et al. Among authors: cotter pd. NPJ Sci Food. 2026 Feb 6;10(1):90. doi: 10.1038/s41538-026-00740-8. NPJ Sci Food. 2026. PMID: 41651877 Free PMC article. Review.

26

GutMicrobiotAware: an international exploratory survey on awareness and understanding of the gut microbiota.

Garcia-Gutierrez E, Arbulu S, Oliver C, Kumar S, Dam SA, Jakobi B, Pennone V, Sarda FAH, Mukherjee A, Cotter PD. Garcia-Gutierrez E, et al. Among authors: cotter pd. Front Microbiol. 2026 Jan 9;16:1643257. doi: 10.3389/fmicb.2025.1643257. eCollection 2025. Front Microbiol. 2026. PMID: 41586364 Free PMC article.

27

Development and Validation of a Food Frequency Questionnaire to Assess Fermented Food Consumption in Adults.

Ferri A, Schneider E, Lucey A, Hennessy Á, Cotter PD, Balasubramanian R, Clarke G, Cryan JF. Ferri A, et al. Among authors: cotter pd. J Hum Nutr Diet. 2026 Feb;39(1):e70183. doi: 10.1111/jhn.70183. J Hum Nutr Diet. 2026. PMID: 41532465 Free PMC article.

28

Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.

FitzGerald JA, Lester KL, O' Sullivan N, Crispie F, Lawton EM, Cotter PD, McNally P, Cox DW. FitzGerald JA, et al. Among authors: cotter pd. J Cyst Fibros. 2026 Mar;25(2):232-239. doi: 10.1016/j.jcf.2025.12.011. Epub 2026 Jan 12. J Cyst Fibros. 2026. PMID: 41530018

29

Optimizing Dietary Fiber Intake: Strategies for Human Nutrition and Food Science.

Walsh SK, Armet AM, Nikolaeva DD, Mota JF, Lucey AJ, Oliero M, Walter J. Walsh SK, et al. Among authors: walter j. Annu Rev Food Sci Technol. 2026 Apr;17(1):25-50. doi: 10.1146/annurev-food-052824-044842. Epub 2026 Jan 12. Annu Rev Food Sci Technol. 2026. PMID: 41525151 Free article. Review.

30

Genomics of Irish swine-derived Streptococcus suis: population structure, prophages and anti-viral defence mechanisms.

Osei EK, O'Mahony AK, O'Hea R, Moriarty J, O'Doherty Á, Wilson M, Garcia Manzanilla E, Mahony J, Kenny JG. Osei EK, et al. Among authors: kenny jg. Microb Genom. 2026 Jan;12(1):001590. doi: 10.1099/mgen.0.001590. Microb Genom. 2026. PMID: 41504765 Free PMC article.

31

Comparing body composition techniques against an adapted multicompartment model in individuals with excess body weight.

Montenegro J, Bennett JP, Oliveira CLP, Berg A, Sharma AM, Mereu L, Shepherd JA, Siervo M, Walter J, Prado CM. Montenegro J, et al. Among authors: walter j. Nutrition. 2026 Mar;143:113033. doi: 10.1016/j.nut.2025.113033. Epub 2025 Nov 21. Nutrition. 2026. PMID: 41475319 Free article.

32

The Microbial Composition of Bovine Colostrum as Influenced by Antibiotic Treatment.

Conboy-Stephenson R, Patangia D, Linehan K, Ross RP, Stanton C. Conboy-Stephenson R, et al. Among authors: stanton c. Antibiotics (Basel). 2025 Dec 3;14(12):1217. doi: 10.3390/antibiotics14121217. Antibiotics (Basel). 2025. PMID: 41463720 Free PMC article.

33

Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.

Xu F, Yang B, Cui S, Yang Z, Dai N, Stanton C, Ross RP, Zhao J, Lai J, Chen W, Wang Y. Xu F, et al. Among authors: stanton c. Food Funct. 2026 Jan 12;17(1):513-530. doi: 10.1039/d5fo04527d. Food Funct. 2026. PMID: 41396034

34

Methanobrevibacter smithii induces postnatal growth retardation through blunting hepatic ketone body metabolism.

Qi M, Song T, Deng Y, Li N, Wang N, Zha A, Ye Q, Wang C, Shao Y, Zhu Y, Sun M, Walter J, Reimer RA, Zhu S, Peng N, Wang J, Yin Y, Zheng J, Tan B. Qi M, et al. Among authors: walter j. Sci Bull (Beijing). 2026 Mar 30;71(6):1302-1306. doi: 10.1016/j.scib.2025.11.039. Epub 2025 Nov 24. Sci Bull (Beijing). 2026. PMID: 41372090 No abstract available.

35

Water kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.

Breselge S, de Paula Dias Moreira L, Skibinska I, Yin X, Brennan L, Kilcawley K, Porcellato D, Cotter PD. Breselge S, et al. Among authors: cotter pd. NPJ Sci Food. 2025 Dec 9;9(1):265. doi: 10.1038/s41538-025-00624-3. NPJ Sci Food. 2025. PMID: 41366253 Free PMC article.

36

Mechanistic insights into microbiome-dependent and personalized responses to dietary fibre in a randomized controlled trial.

Armet AM, Li F, Deehan EC, Nikolaeva DD, Delannoy-Bruno O, Siegwald L, Berger B, Castelli KM, Rodionov DA, Arzamasov AA, Liu J, Seethaler B, Cole JL, Nguyen KN, Jin M, Zhao YY, Sharma AM, Curtis JM, Proctor SD, Bischoff SC, Wismer WV, Osterman AL, Bakal JA, Greiner R, Field CJ, Knights D, Prado CM, Walter J. Armet AM, et al. Among authors: walter j. medRxiv [Preprint]. 2025 Nov 21:2025.11.20.25340625. doi: 10.1101/2025.11.20.25340625. medRxiv. 2025. PMID: 41332831 Free PMC article. Preprint.

37

Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.

Lawrence K, Fibert P, Toribio-Mateas M, Gregory AM, Hobbs J, Quadt F, Wright S, Cotter PD, Patel S, Myrissa K. Lawrence K, et al. Among authors: cotter pd. BMC Psychiatry. 2025 Nov 24;25(1):1117. doi: 10.1186/s12888-025-07568-8. BMC Psychiatry. 2025. PMID: 41286799 Free PMC article. Clinical Trial.

38

Evaluating the rumen microbial community of genetically divergent spring-calving dairy cows grazing grass-only or grass-clover swards at different stages of the grazing season.

Dwan C, Das A, O'Toole PW, O'Callaghan TF, Meehan D, Hennessy D, Irish H, Buckley F, Lahart B. Dwan C, et al. Among authors: o toole pw. Front Microbiol. 2025 Nov 6;16:1642486. doi: 10.3389/fmicb.2025.1642486. eCollection 2025. Front Microbiol. 2025. PMID: 41277963 Free PMC article.

39

Infant gut microbiome reprogramming following introduction of solid foods (weaning).

Ding M, Ross RP, Dempsey E, Li B, Stanton C. Ding M, et al. Among authors: dempsey e, stanton c. Gut Microbes. 2025 Dec 31;17(1):2571428. doi: 10.1080/19490976.2025.2571428. Epub 2025 Nov 9. Gut Microbes. 2025. PMID: 41208251 Free PMC article. Review.

40

Impact of fermented foods consumption on gastrointestinal wellbeing in healthy adults: a systematic review and meta-analysis.

Mukherjee A, Farsi DN, Garcia-Gutierrez E, Akan E, Millan JAS, Angelovski L, Bintsis T, Gérard A, Güley Z, Kabakcı S, Kahala M, Merabti R, Pavli F, Salvetti E, Karagözlü C, Bağlam N, Hyseni B, Bavaro S, Papadimitriou K, Doo EH, Chassard C, Praćer S, Vergères G, Cotter PD, Mojsova S. Mukherjee A, et al. Among authors: cotter pd. Front Nutr. 2025 Oct 10;12:1668889. doi: 10.3389/fnut.2025.1668889. eCollection 2025. Front Nutr. 2025. PMID: 41141260 Free PMC article.

41

Genomic characterisation of recurrent Mycobacterium avium isolates from chronically infected patients reveals patterns of within-host evolution.

Walsh AM, Roycroft E, Hinchion K, Basdeo SA, Sheedy FJ, Crispie F, Cotter PD, McLaughlin AM, Keane J, Fitzgibbon MM, Gleeson LE. Walsh AM, et al. Among authors: cotter pd. Genome Med. 2025 Oct 13;17(1):120. doi: 10.1186/s13073-025-01549-y. Genome Med. 2025. PMID: 41084085 Free PMC article.

42

Health benefits of ethnic fermented foods.

Santa D, Huch M, Stoll DA, Cunedioglu H, Priidik R, Karakaş-Budak B, Matalas A, Pennone V, Girija A, Arranz E, Syrpas M, Mukherjee A, Cotter PD, Mojsova S, Chassard C, Praćer S, Vergères G, Kütt ML. Santa D, et al. Among authors: cotter pd. Front Nutr. 2025 Sep 26;12:1677478. doi: 10.3389/fnut.2025.1677478. eCollection 2025. Front Nutr. 2025. PMID: 41080174 Free PMC article.

43

In vitro assessment of bacterial supernatants on hypothalamic gene expression: implications for appetite regulation.

Cuesta-Marti C, Valderrama B, Bastiaanssen T, Cryan JF, Stanton C, O'Mahony SM, Clarke G, Schellekens H. Cuesta-Marti C, et al. Among authors: stanton c. NPJ Biofilms Microbiomes. 2025 Oct 3;11(1):192. doi: 10.1038/s41522-025-00820-9. NPJ Biofilms Microbiomes. 2025. PMID: 41044088 Free PMC article.

44

Stress and depression risk in pregnancy associates with altered immune function.

Mealy G, Hempelmann Perez S, Brennan K, Callanan S, Saldova R, Groeger D, Van Sinderen D, Cotter PD, Doyle SL, McAuliffe FM. Mealy G, et al. Among authors: cotter pd. World J Biol Psychiatry. 2025 Oct;26(8):346-358. doi: 10.1080/15622975.2025.2530000. Epub 2025 Jul 26. World J Biol Psychiatry. 2025. PMID: 41021330 Free article.

45

Effects of lyophilised faecal filtrate compared with lyophilised donor stool on Clostridioides difficile recurrence: a multicentre, randomised, double-blinded, non-inferiority trial.

Kao D, Wong K, Lee C, Steiner T, Franz R, McDougall C, Silva M, Schmidt TSB, Walter J, Loebenberg R, Monaghan TM, Giebelhaus RT, Harynuk JJ, Xu H, Yaskina M, MacDonald KV, Marshall DA, Louie T. Kao D, et al. Among authors: walter j. Lancet Gastroenterol Hepatol. 2025 Nov;10(11):986-997. doi: 10.1016/S2468-1253(25)00190-6. Epub 2025 Sep 22. Lancet Gastroenterol Hepatol. 2025. PMID: 40997843 Clinical Trial.

46

Iron-saturated bovine lactoferrin preserves microbiota diversity and healthy ageing-associated taxa in an in vitro colon model of elderly gut microbiota (Iron-saturated bovine lactoferrin impact on elderly gut microbiota).

Ruiz-Rico M, Ye H, O'Callaghan TF, O'Toole PW, McCarthy EK. Ruiz-Rico M, et al. Among authors: o toole pw. PLoS One. 2025 Sep 17;20(9):e0332631. doi: 10.1371/journal.pone.0332631. eCollection 2025. PLoS One. 2025. PMID: 40961038 Free PMC article.

47

Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics.

Peña N, Lafuente I, Sevillano E, Feito J, Allendez G, Muñoz-Atienza E, Crispie F, Cintas LM, Cotter PD, Hernández PE, Borrero J. Peña N, et al. Among authors: cotter pd. Genes (Basel). 2025 Aug 11;16(8):946. doi: 10.3390/genes16080946. Genes (Basel). 2025. PMID: 40869994 Free PMC article.

48

Microbial Sharing Between Siblings Supports Metabolic Functions Protective Against Allergy.

Devotta H, Lavelle A, Korpela K, Hurley S, Shannon E, Lunjani N, Ambikan A, Neogi U, Venter C, Walter J, Hourihane J, O'Mahony L. Devotta H, et al. Among authors: walter j. Allergy. 2025 Oct;80(10):2934-2937. doi: 10.1111/all.70033. Epub 2025 Aug 29. Allergy. 2025. PMID: 40879391 Free PMC article. No abstract available.

49

Understanding Exopolysaccharides from Lactic Acid Bacteria: Synthesis, Functions, and Applications.

Li H, Jin Y, Li H, Zhao J, Stanton C, Ross RP, Chen W, Yang B. Li H, et al. Among authors: stanton c. J Agric Food Chem. 2025 Sep 10;73(36):22110-22132. doi: 10.1021/acs.jafc.5c04613. Epub 2025 Aug 29. J Agric Food Chem. 2025. PMID: 40878626 Review.

50

Perinatal factors influencing the earliest establishment of the infant microbiome.

Linehan K, Healy K, Hurley E, O'Shea CA, Ryan CA, Ross RP, Stanton C, Dempsey EM. Linehan K, et al. Among authors: stanton c, dempsey em. Microbiome Res Rep. 2025 Jun 12;4(2):24. doi: 10.20517/mrr.2024.92. eCollection 2025. Microbiome Res Rep. 2025. PMID: 40852123 Free PMC article.

51

Assessment of absolute abundance in mother-infant gut microbiome using marine-sourced bacterial DNA spike-in and comparison with conventional quantification methods.

Wang S, Healy D, Patangia D, Uniacke-Lowe S, Kamilari E, Kozak IM, Yang B, Dempsey EM, Stanton C, Ross RP. Wang S, et al. Among authors: stanton c, dempsey em. Microbiome Res Rep. 2025 Jun 9;4(2):23. doi: 10.20517/mrr.2024.94. eCollection 2025. Microbiome Res Rep. 2025. PMID: 40852122 Free PMC article.

52

Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.

Davies RG, Wood LA, Hengist A, O'Donovan C, Barton W, Crispie F, Walhin JP, Valdivia-Garcia MA, Garcia-Perez I, Frost G, O'Sullivan O, Cotter PD, Gonzalez JT, Betts JA, Koumanov F, Thompson D. Davies RG, et al. Among authors: o sullivan o, cotter pd. J Physiol. 2025 Dec;603(24):7731-7750. doi: 10.1113/JP287424. Epub 2025 Aug 19. J Physiol. 2025. PMID: 40828642 Free PMC article. Clinical Trial.

53

Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.

Pan Z, Walsh CJ, Feehily C, Nori SRC, McAuliffe FM, Cotter PD, MacSharry J, van Sinderen D. Pan Z, et al. Among authors: cotter pd. Gut Microbes. 2025 Dec;17(1):2541033. doi: 10.1080/19490976.2025.2541033. Epub 2025 Aug 4. Gut Microbes. 2025. PMID: 40755225 Free PMC article.

54

Protocol: Scoping review of the association between complementary feeding, growth, and immune health in infants and toddlers-An EAACI guideline paper.

Venter C, Alonso-Coello P, Beltran J, Bracchiglione J, Fernandez-Saenz K, Riera P, Solà I, Arasi S, Berni Canani R, Fleischer D, Eguíluz-Gracia I, Meyer R, Roberts G, Roth-Walter F, Santos AF, Skypala I, Smith PK, Sokolowska M, Torres MJ, Vassilopoulou E, Walter J, O'Mahony L. Venter C, et al. Among authors: walter j. Pediatr Allergy Immunol. 2025 Aug;36(8):e70145. doi: 10.1111/pai.70145. Pediatr Allergy Immunol. 2025. PMID: 40747578

55

The food-associated resistome is shaped by processing and production environments.

Quijada NM, Cobo-Díaz JF, Valentino V, Barcenilla C, De Filippis F, Cabrera-Rubio R, Carlino N, Pinto F, Dzieciol M, Calvete-Torre I, Sabater C, Rubino F, Knobloch S, Skirnisdottir S, Ruiz L, López M, Prieto M, Marteinsson VT, Margolles A, Segata N, Cotter PD, Wagner M, Ercolini D, Alvarez-Ordóñez A. Quijada NM, et al. Among authors: cotter pd. Nat Microbiol. 2025 Aug;10(8):1854-1867. doi: 10.1038/s41564-025-02059-8. Epub 2025 Jul 30. Nat Microbiol. 2025. PMID: 40739039 Free PMC article.

56

Development of a bio-functional fermented soy beverage supplemented with microbial exopolysaccharides and its effect on the human gut microbiome in vitro.

Bisson G, Comuzzi C, FitzGerald JA, Mukherjee A, Renoldi N, Innocente N, Beresford T, Mathur H, Cotter PD, Marino M. Bisson G, et al. Among authors: cotter pd. Food Funct. 2025 Jul 28;16(15):6203-6212. doi: 10.1039/d5fo01288k. Food Funct. 2025. PMID: 40674041

57

Late-onset sepsis treatment in very preterm infants alters longitudinal microbiome trajectory with lower abundance of Bifidobacterium despite probiotic supplementation.

Healy DB, Wang S, Patangia D, Grimaud G, Ross RP, Stanton C, Dempsey EM. Healy DB, et al. Among authors: stanton c, dempsey em. Gut Microbes. 2025 Dec;17(1):2523808. doi: 10.1080/19490976.2025.2523808. Epub 2025 Jul 6. Gut Microbes. 2025. PMID: 40618372 Free PMC article.

58

Intestinal pH: a major driver of human gut microbiota composition and metabolism.

Brinck JE, Sinha AK, Laursen MF, Dragsted LO, Raes J, Uribe RV, Walter J, Roager HM, Licht TR. Brinck JE, et al. Among authors: walter j. Nat Rev Gastroenterol Hepatol. 2025 Sep;22(9):639-656. doi: 10.1038/s41575-025-01092-6. Epub 2025 Jul 2. Nat Rev Gastroenterol Hepatol. 2025. PMID: 40603778 Review.

59

Optimising White Wheat Bread Fortification with Vitamin D₃ and Dietary Fibre: Balancing Nutritional Enhancement and Technological Quality.

Boudrag S, Arendt EK, Segura Godoy C, Sahin AW, Nyhan L, Cashman KD, Zannini E. Boudrag S, et al. Among authors: arendt ek. Foods. 2025 Jun 11;14(12):2055. doi: 10.3390/foods14122055. Foods. 2025. PMID: 40565664 Free PMC article.

60

A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset.

Zhang E, Breselge S, Carlino N, Segata N, Claesson MJ, Cotter PD. Zhang E, et al. Among authors: cotter pd. iScience. 2025 Mar 1;28(4):112139. doi: 10.1016/j.isci.2025.112139. eCollection 2025 Apr 18. iScience. 2025. PMID: 40463955 Free PMC article.

61

Gut and oral microbial profile associations to oral cancer.

Nayyar J, Bedu-Ferrari C, Patangia D, Hurley E, Feeley L, Ross RP, Stanton C, Brady P. Nayyar J, et al. Among authors: stanton c. J Dent. 2025 Sep;160:105848. doi: 10.1016/j.jdent.2025.105848. Epub 2025 May 31. J Dent. 2025. PMID: 40456384

62

A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.

Meehan DE, O'Toole PW. Meehan DE, et al. Among authors: o toole pw. Microb Ecol. 2025 May 27;88(1):54. doi: 10.1007/s00248-025-02551-y. Microb Ecol. 2025. PMID: 40423805 Free PMC article. Review.

63

Exploring tarhana's prebiotic potential using different flours in an in vitro fermentation model.

Koc F, Sabuncu M, Yavuz GG, Düven G, Abdo RMK, Bağci U, Şahan Y, Özmen Toğay S, Ross RP, Stanton C. Koc F, et al. Among authors: stanton c. Food Funct. 2025 Jun 16;16(12):4754-4771. doi: 10.1039/d5fo00486a. Food Funct. 2025. PMID: 40422929

64

Gene-trait matching among Bifidobacterium dentium strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.

Catalano Gonzaga O, McKenna S, O'Neill I, Cotter PD, McAuliffe FM, Coffey A, van Sinderen D, Bottacini F. Catalano Gonzaga O, et al. Among authors: cotter pd. Front Microbiol. 2025 May 12;16:1584694. doi: 10.3389/fmicb.2025.1584694. eCollection 2025. Front Microbiol. 2025. PMID: 40421466 Free PMC article.

65

Effects of feeding a simulated waste milk on growth, health, fecal microbiota, and antibiotic resistance in dairy heifer calves.

Flynn A, Barton W, McAloon C, McFadden M, Crispie F, McPherson SE, Allendez G, Murphy JP, McAloon CG, Cotter PD, Kennedy E. Flynn A, et al. Among authors: cotter pd. J Dairy Sci. 2025 Aug;108(8):8710-8725. doi: 10.3168/jds.2024-26062. Epub 2025 May 16. J Dairy Sci. 2025. PMID: 40383390 Free article.

66

Effects of Prebiotics and a Synthetic Microbiome Consortium on the Composition and Metabolites of the Elderly Gut Microbiota In Vitro.

Ye H, Meehan D, Timmons S, O'Toole PW. Ye H, et al. Among authors: o toole pw. J Agric Food Chem. 2025 May 14;73(19):11720-11729. doi: 10.1021/acs.jafc.5c00364. Epub 2025 May 5. J Agric Food Chem. 2025. PMID: 40324006 Free PMC article.

67

Bacteroides maternus sp. nov., a novel species isolated from human faeces.

da Silva Morais E, Grimaud GM, Warda A, Stephens N, Ross RP, Stanton C. da Silva Morais E, et al. Among authors: stanton c. Sci Rep. 2025 Apr 21;15(1):13808. doi: 10.1038/s41598-025-96846-2. Sci Rep. 2025. PMID: 40258876 Free PMC article.

68

OPTIMATRIX v2.0: Optimised protocol to mitigate microbial blooms in the micro-Matrix bioreactor platform used as an ex vivo human distal colon model.

Mukherjee A, Leali NF, Salvetti E, Torriani S, Cotter PD, Mathur H. Mukherjee A, et al. Among authors: cotter pd. MethodsX. 2025 Mar 22;14:103275. doi: 10.1016/j.mex.2025.103275. eCollection 2025 Jun. MethodsX. 2025. PMID: 40224146 Free PMC article.

69

The effects of offering adequate-quality or high-quality colostrum on the passive immunity, health, growth, and fecal microbiome development of dairy heifer calves.

Flynn A, Leech J, McFadden M, McAloon C, Murphy JP, Crispie F, Cotter PD, McAloon C, Kennedy E. Flynn A, et al. Among authors: cotter pd. J Dairy Sci. 2025 Jun;108(6):6254-6272. doi: 10.3168/jds.2024-26165. Epub 2025 Apr 11. J Dairy Sci. 2025. PMID: 40221038 Free article.

70

Regional microbial content of fermented traditional and industrial East Mediterranean sausages from the islands of Cyprus and Mytilini.

Kamilari E, Stanton C, Tsaltas D, Ross RP. Kamilari E, et al. Among authors: stanton c. Microbiome Res Rep. 2024 Oct 28;4(1):3. doi: 10.20517/mrr.2024.47. eCollection 2025. Microbiome Res Rep. 2024. PMID: 40207283 Free PMC article.

71

Lactobacillus johnsonii CCFM1376 improves hypercholesterolemia in mice by regulating the composition of bile acids.

Chen K, Dang D, Li H, Ross RP, Stanton C, Chen W, Yang B. Chen K, et al. Among authors: stanton c. Microbiome Res Rep. 2024 Nov 9;4(1):6. doi: 10.20517/mrr.2024.38. eCollection 2025. Microbiome Res Rep. 2024. PMID: 40207276 Free PMC article.

72

A blueprint for contemporary studies of microbiomes.

Bindels LB, Watts JEM, Theis KR, Carrion VJ, Ossowicki A, Seifert J, Oh J, Shao Y, Hilty M, Kumar P, Hildebrand F, Lovejoy C, Wigley P, Yu K, Zhang M, Zhang T, Walter J, Desai MS, Huws SA, Schriml LM, Ravel J, Fricke WF, Eloe-Fadrosh EA, Lee CK, Clavel T. Bindels LB, et al. Among authors: walter j. Microbiome. 2025 Apr 8;13(1):95. doi: 10.1186/s40168-025-02091-0. Microbiome. 2025. PMID: 40200306 Free PMC article.

73

Cottage cheese, a relatively underexplored cultured dairy product with potential health benefits?

Farsi DN, Mathur H, Beresford T, Cotter PD. Farsi DN, et al. Among authors: cotter pd. Crit Rev Food Sci Nutr. 2025;65(32):7953-7963. doi: 10.1080/10408398.2025.2487682. Epub 2025 Apr 6. Crit Rev Food Sci Nutr. 2025. PMID: 40188423 Free article. Review.

74

Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.

Tarracchini C, Lordan C, Milani C, Moreira LPD, Alabedallat QM, de Moreno de LeBlanc A, Turroni F, Lugli GA, Mancabelli L, Longhi G, Brennan L, Mahony J, LeBlanc JG, Nilaweera KN, Cotter PD, van Sinderen D, Ventura M. Tarracchini C, et al. Among authors: cotter pd. Microbiol Mol Biol Rev. 2025 Jun 25;89(2):e0018423. doi: 10.1128/mmbr.00184-23. Epub 2025 Apr 2. Microbiol Mol Biol Rev. 2025. PMID: 40172109 Free PMC article. Review.

75

Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics.

Osei EK, O'Hea R, Cambillau C, Athalye A, Hille F, Franz CMAP, O'Doherty Á, Wilson M, Murray GGR, Weinert LA, Manzanilla EG, Mahony J, Kenny JG. Osei EK, et al. Among authors: kenny jg. Microbiol Res. 2025 Jul;296:128147. doi: 10.1016/j.micres.2025.128147. Epub 2025 Mar 21. Microbiol Res. 2025. PMID: 40132484 Free article.

76

Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.

Nori SRC, Walsh CJ, McAuliffe FM, Moore RL, Van Sinderen D, Feehily C, Cotter PD. Nori SRC, et al. Among authors: cotter pd. NPJ Biofilms Microbiomes. 2025 Mar 23;11(1):49. doi: 10.1038/s41522-025-00682-1. NPJ Biofilms Microbiomes. 2025. PMID: 40122890 Free PMC article.

77

aurora: a machine learning gwas tool for analyzing microbial habitat adaptation.

Bujdoš D, Walter J, O'Toole PW. Bujdoš D, et al. Among authors: o toole pw, walter j. Genome Biol. 2025 Mar 23;26(1):66. doi: 10.1186/s13059-025-03524-7. Genome Biol. 2025. PMID: 40122838 Free PMC article.

78

The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.

Breselge S, Skibinska I, Yin X, Brennan L, Kilcawley K, Cotter PD. Breselge S, et al. Among authors: cotter pd. Commun Biol. 2025 Mar 11;8(1):415. doi: 10.1038/s42003-025-07808-3. Commun Biol. 2025. PMID: 40069560 Free PMC article.

79

Fiber Intervention Study in Prader-Willi Syndrome: Insights into Metabolic and Microbiota Shifts.

Tan Q, Peng Y, Deehan EC, Vieira FT, Ho BWP, Afhami S, Wine E, Madsen KL, Field CJ, Pakseresht M, Ilkayeva O, Newgard CB, Walter J, Tun HM, Haqq AM. Tan Q, et al. Among authors: walter j. J Clin Endocrinol Metab. 2025 Oct 16;110(11):3120-3132. doi: 10.1210/clinem/dgaf142. J Clin Endocrinol Metab. 2025. PMID: 40036959 Free PMC article.

80

A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research.

Metwaly A, Kriaa A, Hassani Z, Carraturo F, Druart C; IHMCSA Consortium; Arnauts K, Wilmes P, Walter J, Rosshart S, Desai MS, Dore J, Fasano A, Blottiere HM, Maguin E, Haller D. Metwaly A, et al. Among authors: walter j. Nat Rev Gastroenterol Hepatol. 2025 May;22(5):343-356. doi: 10.1038/s41575-025-01041-3. Epub 2025 Mar 3. Nat Rev Gastroenterol Hepatol. 2025. PMID: 40033063 Review.

81

Toward a health-associated core keystone index for the human gut microbiome.

Goel A, Shete O, Goswami S, Samal A, C B L, Kedia S, Ahuja V, O'Toole PW, Shanahan F, Ghosh TS. Goel A, et al. Among authors: o toole pw. Cell Rep. 2025 Mar 25;44(3):115378. doi: 10.1016/j.celrep.2025.115378. Epub 2025 Mar 1. Cell Rep. 2025. PMID: 40023840 Free article.

82

Bactofencin A Displays a Delayed Killing Effect on a Clinical Strain of Staphylococcus aureus Which Is Greatly Accelerated in the Presence of Nisin.

O'Connor PM, Cotter PD, Hill C, Ross RP. O'Connor PM, et al. Among authors: cotter pd. Antibiotics (Basel). 2025 Feb 11;14(2):184. doi: 10.3390/antibiotics14020184. Antibiotics (Basel). 2025. PMID: 40001428 Free PMC article.

83

A secondary metabolite of Limosilactobacillusreuteri R2lc drives strain-specific pathology in a spontaneous mouse model of multiple sclerosis.

Archer D, Pérez-Muñoz ME, Tollenaar S, Veniamin S, Hotte N, Cheng CC, Nieves K, Oh JH, Morceli L, Muncner S, Barreda DR, Krishnamoorthy G, Power C, van Pijkeren JP, Walter J. Archer D, et al. Among authors: walter j. Cell Rep. 2025 Mar 25;44(3):115321. doi: 10.1016/j.celrep.2025.115321. Epub 2025 Feb 21. Cell Rep. 2025. PMID: 39985770 Free article.

84

Leuconostoc lactis strain APC 3969 produces a new variant of cyclic bacteriocin leucocyclicin Q and displays potent anti-Clostridium perfringens activity.

de Farias FM, Soria MC, O'Connor PM, Huang X, Buttimer C, Kamilari E, Deliephan A, Hill D, Fursenko O, Wiese J, Draper L, Stanton C, Hill C, Ross RP. de Farias FM, et al. Among authors: stanton c. Sci Rep. 2025 Feb 21;15(1):6372. doi: 10.1038/s41598-025-89450-x. Sci Rep. 2025. PMID: 39984510 Free PMC article.

85

In vitro digestibility of bioprocessed brewer's spent yeast: Demonstrating protein quality and gut microbiome modulation potential.

Jaeger A, Nyhan L, Sahin AW, Zannini E, Meehan D, Li J, O'Toole PW, Arendt EK. Jaeger A, et al. Among authors: o toole pw, arendt ek. Food Res Int. 2025 Feb;202:115732. doi: 10.1016/j.foodres.2025.115732. Epub 2025 Jan 11. Food Res Int. 2025. PMID: 39967179 Free article.

86

Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.

O' Donovan CM, Nori SRC, Shanahan F, Celentano G, Murphy TB, Cotter PD, Sullivan OO. O' Donovan CM, et al. Among authors: cotter pd. Sci Rep. 2025 Feb 15;15(1):5619. doi: 10.1038/s41598-025-88723-9. Sci Rep. 2025. PMID: 39955324 Free PMC article.

87

Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation.

Chen Y, Fang H, Chen H, Liu X, Zhao J, Stanton C, Ross RP, Chen W, Yang B. Chen Y, et al. Among authors: stanton c. Gut Microbes. 2025 Dec;17(1):2464945. doi: 10.1080/19490976.2025.2464945. Epub 2025 Feb 9. Gut Microbes. 2025. PMID: 39924893 Free PMC article.

88

Streptococcus wuxiensis sp. nov., Streptococcus jiangnanensis sp. nov. and Streptococcus fermentans sp. nov.: three novel species of genus Streptococcus isolated from human breast milk.

Zhou Y, Zhao J, Ross P, Stanton C, Chen W, Yang B. Zhou Y, et al. Among authors: stanton c. Int J Syst Evol Microbiol. 2025 Feb;75(2). doi: 10.1099/ijsem.0.006674. Int J Syst Evol Microbiol. 2025. PMID: 39918554

89

Human milk oligosaccharides 2'-fucosyllactose and 3-fucosyllactose attenuate ovalbumin-induced food allergy through immunoregulation and gut microbiota modulation.

Wu S, Chen H, Yu R, Li H, Zhao J, Stanton C, Paul Ross R, Chen W, Yang B. Wu S, et al. Among authors: stanton c. Food Funct. 2025 Feb 17;16(4):1267-1283. doi: 10.1039/d4fo04638b. Food Funct. 2025. PMID: 39918321

90

Targeting the Gut-Heart Axis Improves Cardiac Remodeling in a Clinical Scale Model of Cardiometabolic Syndrome.

Herisson FM, Cluzel GL, Llopis-Grimalt MA, O'Donovan AN, Koc F, Karnik K, Laurie I, Canene-Adams K, Ross RP, Stanton C, Caplice NM. Herisson FM, et al. Among authors: stanton c. JACC Basic Transl Sci. 2024 Nov 20;10(1):1-15. doi: 10.1016/j.jacbts.2024.09.004. eCollection 2025 Jan. JACC Basic Transl Sci. 2024. PMID: 39906593 Free PMC article.

91

Rebuttal to Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).

Stanton C, Koc F, Kelleher S, Ross P, Magnier C, McMahon CJ. Stanton C, et al. Pediatr Cardiol. 2025 Apr;46(4):1129-1130. doi: 10.1007/s00246-025-03795-8. Epub 2025 Feb 3. Pediatr Cardiol. 2025. PMID: 39900806 No abstract available.

92

Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.

Kennedy EC, Ross FC, O'Shea CA, Lavelle A, Ross P, Dempsey E, Stanton C, Hawkes CP. Kennedy EC, et al. Among authors: dempsey e, stanton c. BMJ Open. 2025 Jan 30;15(1):e089206. doi: 10.1136/bmjopen-2024-089206. BMJ Open. 2025. PMID: 39890137 Free PMC article.

93

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation.

Li F, Armet AM, Korpela K, Liu J, Quevedo RM, Asnicar F, Seethaler B, Rusnak TBS, Cole JL, Zhang Z, Zhao S, Wang X, Gagnon A, Deehan EC, Mota JF, Bakal JA, Greiner R, Knights D, Segata N, Bischoff SC, Mereu L, Haqq AM, Field CJ, Li L, Prado CM, Walter J. Li F, et al. Among authors: walter j. Cell. 2025 Mar 6;188(5):1226-1247.e18. doi: 10.1016/j.cell.2024.12.034. Epub 2025 Jan 23. Cell. 2025. PMID: 39855197 Free article. Clinical Trial.

94

Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus.

MacCann R, Li J, Leon AAG, Negi R, Alalwan D, Tinago W, McGettrick P, Cotter AG, Landay A, Sabin C, O'Toole PW, Mallon PWG; Understanding the Pathology of Comorbid Disease in HIV-Infected Individuals (HIV UPBEAT) Study Group. MacCann R, et al. Among authors: o toole pw. J Infect Dis. 2025 Apr 15;231(4):e781-e791. doi: 10.1093/infdis/jiaf043. J Infect Dis. 2025. PMID: 39854172 Free PMC article.

95

Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.

Srinivas M, Walsh CJ, Crispie F, O'Sullivan O, Cotter PD, van Sinderen D, Kenny JG. Srinivas M, et al. Among authors: kenny jg, o sullivan o, cotter pd. Sci Rep. 2025 Jan 22;15(1):2822. doi: 10.1038/s41598-024-83410-7. Sci Rep. 2025. PMID: 39843557 Free PMC article.

96

Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics.

Osei EK, O'Hea R, Cambillau C, Athalye A, Hille F, Franz CMAP, O'Doherty Á, Wilson M, Murray GGR, Weinert LA, Manzanilla EG, Mahony J, Kenny JG. Osei EK, et al. Among authors: kenny jg. bioRxiv [Preprint]. 2025 Jan 7:2025.01.07.631744. doi: 10.1101/2025.01.07.631744. bioRxiv. 2025. Update in: Microbiol Res. 2025 Jul;296:128147. doi: 10.1016/j.micres.2025.128147. PMID: 39829746 Free PMC article. Updated. Preprint.

97

Pediococcus acidilactici CECT 9879 (pA1c®) and heat inactivated pA1c® (pA1c® HI) ameliorate gestational diabetes mellitus in mice.

Yavorov-Dayliev D, Milagro FI, Ayo J, Oneca M, Goyache I, López-Yoldi M, FitzGerald JA, Crispie F, Cotter PD, Aranaz P. Yavorov-Dayliev D, et al. Among authors: cotter pd. Life Sci. 2025 Feb 1;362:123359. doi: 10.1016/j.lfs.2024.123359. Epub 2025 Jan 4. Life Sci. 2025. PMID: 39761739 Free article.

98

Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome.

Wosinska L, Walsh LH, Walsh CJ, Cotter PD, Guinane CM, O'Sullivan O. Wosinska L, et al. Among authors: o sullivan o, cotter pd. Microbiome Res Rep. 2024 Jul 22;3(4):41. doi: 10.20517/mrr.2023.69. eCollection 2024. Microbiome Res Rep. 2024. PMID: 39741946 Free PMC article.

99

The impact of exposure to green or bluespace on dietary intake and food choices among adults-A systematic literature review.

Gilbourne CA, Scarry A, Tierney AC, O'Connor EM. Gilbourne CA, et al. Among authors: o connor em. Food Sci Nutr. 2024 Nov 4;12(12):9913-9927. doi: 10.1002/fsn3.4447. eCollection 2024 Dec. Food Sci Nutr. 2024. PMID: 39723100 Free PMC article. Review.

100

Differential cortical aspartate uptake across the oestrous cycle is associated with changes in gut microbiota in Wistar-Kyoto rats.

Sajjad J, Morael J, Melo TG, Foley T, Murphy A, Keane J, Popov J, Stanton C, Dinan TG, Clarke G, Cryan JF, Collins JM, O'Mahony SM. Sajjad J, et al. Among authors: stanton c. Neurosci Lett. 2025 Jan 31;847:138096. doi: 10.1016/j.neulet.2024.138096. Epub 2024 Dec 21. Neurosci Lett. 2025. PMID: 39716584

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