Publications

Track updates and links on Google Scholar.

Preprints

  • M Fernández-Niño, LA Wessjohann, JM Guillamón, D Burgos-Toro, S Moriano-Gutierrez, G Di Matteo, Z Islam, R van Tatenhove-Pel, VR Marcelino, R Ledesma-Amaro. From circuits to symphonies: redefining synthetic biology for multimicrobial systems. Preprint. DOI: 10.20944/preprints202509.1416.v1
  • VW Salazar, H Verbruggen, VR Marcelino#, K-A Lê Cao# (#co-senior authors). Global picoplankton biogeography revealed by metagenomic and climatic data integration. bioRxiv; 2024-11. DOI: 10.1101/2024.11.23.624595

2026

  • Y Tong, VR Marcelino, R Turnbull, H Verbruggen. ChloroScan: Recovering plastid genome bins from metagenomic data. Molecular Ecology Resources 2026; 26, e70143. DOI: 10.1111/1755-0998.70143

2025

  • Y Shi1, Y Li1, H Li1, A Haerheng1, VR Marcelino1, M Lu, P Lemey1, J Tang, Y Bi, JH Pettersson1, J Bohlin1, J Klaps, Z Wu, W Wan, B Sun, M Kang, EC Holmes1, N He, S Su. Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance. CELL 2025; 23, 6591–6605.e14. (1equal contribution).
  • C Welsh, PR Cabotaje, VR Marcelino, TD Watts, DJ Kountz, M Jespersen, JA Gould, NQ Doan, JP Lingford, T Koralegedara, J Solari, GL D'Adamo, P Huang, N Bong, EL Gulliver, RB Young, H Land, K Walter, I Cann, GV Pereira, EC Martens, PG Wolf, JM Ridlon, HR Gaskins, EM Giles, D Lyras, R Lappan, G Berggren, SC Forster, C Greening. A widespread hydrogenase drives fermentative growth of gut bacteria in healthy people. Nature Microbiology 2025; 10, 2686–2701.
  • A Bachem, M Clarke, G Kong, I Tarasova, L Dryburgh, L Kosack, AR Lee, LD Newland, T Wagner, E Bawden, KM Yap, MD Wilson, S Engel, KR Wilson, BE Russ, K Tandon, PKH Lau, G McArthur, VR Marcelino, PA Beavis, SJ Turner, J Waithman, TP Stinear, S Sandhu, J Schröder, T Gebhardt, S Bedoui. SCFA producing capabilities of the gut microbiota enhance tumor-specific CD127+CD8+ T cell immunity against melanoma. Immunity 2025; 58(11) 2799–2813.
  • PT Clausen, HB Hallgren, S Overballe-Petersen, VR Marcelino, H Hasman, FM Aarestrup. Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA. NAR Genomics and Bioinformatics 2025; 7(3), lqaf116.
  • H Koceva, M Amiratashani, P Akbarimoghaddam, B Hoffmann, G Zhurgenbayeva, MS Gresnigt, VR Marcelino, C Eggeling, MT Figge, M-J Amorim, AS Mosig. Deciphering respiratory viral infections by harnessing organ-on-chip technology to explore the gut–lung axis. Open Biology 2025; 15(3), 240231.
  • A Day, R Slater, VR Marcelino, R Wheeler, R Young, N Maddigan, S Forster, S Costello, W Uylaki, C Probert, J Andrews, CK Yao, P Gibson, R Bryant. Deep functional analysis of a defined sulphide-reducing diet (4-SURE diet) as a novel therapy for ulcerative colitis (UC) demonstrates all specific luminal micro environmental objectives were achieved. Inflammatory Bowel Diseases 2025; 31(11), 3160–3171.

2024

  • LK Boelsen, MJ Williams, YTM Mangwiro, H Hansji, A Czajko, VR Marcelino, S Forster, JM Said, C Satzke, R Saffery. The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy. Scientific Reports 2024; 14(1), 19318.

2023

  • VR Marcelino*. Gut health: the value of connections. eLife 2023; 12, e92319.
  • VR Marcelino*, C Welsh, C Diener, EL Gulliver, EL Rutten, RB Young, EM Giles, SM Gibbons, C Greening, SC Forster. Disease-specific loss of microbial cross-feeding interactions in the human gut. Nature Communications 2023; 14, 6546.
  • VW Salazar, B Shabban, MM Quiroga, R Turnbull, E Tescari, VR Marcelino, H Verbruggen, K-A Lê Cao. Metaphor – A workflow for streamlined assembly and binning of metagenomes. GigaScience 2023; 12, giad055.
  • VR Marcelino*, C Birnbaum. AusME 2022 Melbourne conference. Microbiology Australia 2023; 44, 3–4.
  • SA Marshall, RB Young, JM Lewis, EL Rutten, J Gould, CK Barlow, C Giogha, VR Marcelino, N Fields, RB Schittenhelm, EL Hartland, NE Scott, SC Forster, EL Gulliver. The broccoli-derived antioxidant sulforaphane changes the growth of gastrointestinal microbiota, allowing for the production of anti-inflammatory metabolites. Journal of Functional Foods 2023; 107, 105645.
  • GL D'Adamo, M Chonwerawong, LJ Gearing, VR Marcelino, JA Gould, EL Rutten, SM Solari, PWR Khoo, TJ Wilson, T Thomason, EL Gulliver, PJ Hertzog, EM Giles, SC Forster. Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease. Cell Reports Medicine 2023; 4:101124.
  • EL Gulliver, V Adams, VR Marcelino, J Gould, EL Rutten, DR Powell, RB Young, GL D'Adamo, J Hemphill, SM Solari, SA Revitt-Mills, S Munn, T Jirapanjawat, C Greening, JC Boer, KL Flanagan, M Kaldhusdal, M Plebanski, KB Gibney, RJ Moore, JI Rood, SC Forster. Extensive genome analysis identifies novel plasmid families in Clostridium perfringens. Microbial Genomics 2023; 9: mgen000995.

2022

  • SM Solari, RB Young, VR Marcelino, SC Forster. expam—high-resolution analysis of metagenomes using distance trees. Bioinformatics 2022; btac591.
  • EL Gulliver, RB Young, M Chonwerawong, GL D'Adamo, T Thomason, JT Widdop, EL Rutten, VR Marcelino, RV Bryant, SP Costello, CL O'Brien, GL Hold, EM Giles, SC Forster. The future of microbiome-based therapeutics. Alimentary Pharmacology & Therapeutics 2022; 00: 1–17.
  • MM Pasella, M-FE Lee, VR Marcelino, A Willis, H Verbruggen. Ten Ostreobium (Ulvophyceae) strains from Great Barrier Reef corals as a resource for algal endolith biology and genomics. Phycologia 2022; 61:452–458.
  • F Meyer, A Fritz, Z-L Deng et al. Critical Assessment of Metagenome Interpretation – the second round of challenges. Nature Methods 2022; 19: 429–440.
  • ACM Teixeira, VR Marcelino, J Alexandrino, CFB Haddad, AA Giaretta. Populational differentiation in Boana bischoffi (Anura, Hylidae): revisiting the issue using molecular, morphological, and acoustic data. Journal of Herpetology 2022; 56: 110–119.
  • T Jia, WS Chang, VR Marcelino, S Zhao, X Liu, Y You, EC Holmes, M Shi, C Zhang. Characterization of the gut microbiome and resistomes of wild and zoo-captive macaques. Frontiers in Veterinary Science 2022; 8:778556.

2021

  • R Young, VR Marcelino, M Chonwerawong, EL Gulliver, SC Forster. Key Technologies for Progressing Discovery of Microbiome-Based Medicines. Frontiers in Microbiology 2021; 12:1604.
  • B Jones-Freeman, M Chonwerawong, VR Marcelino, AV Deshpande, SC Forster, MR Starkey. The microbiome and host mucosal interactions in urinary tract diseases. Mucosal Immunology 2021; 14:1–4.
  • C Iha, JA Varela, V Avila, CJ Jackson, KA Bogaert, Y Chen, LM Judd, RR Wick, KE Holt, MM Pasella, F Ricci, SI Repetti, M Medina, VR Marcelino, CX Chan, H Verbruggen. Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Current Biology 2021; 31:1393–1402.

2020 and earlier

  • J Charon, VR Marcelino, R Wetherbee, H Verbruggen, EC Holmes. Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae cultures. Viruses 2020; 12:1180.
  • VR Marcelino*, EC Holmes, TC Sorrell. The use of taxon-specific reference databases compromises metagenomic classification. BMC Genomics 2020; 21:184.
  • VR Marcelino*, PTLC Clausen, JP Buchmann, M Wille, JR Iredell, W Meyer, O Lund, TC Sorrell, EC Holmes. CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data. Genome Biology 2020; 21:103.
  • A Góes-Neto, VR Marcelino, H Verbruggen, FF da Silva, F Badotti. Biodiversity of endolithic fungi in coral skeletons and other reef substrates revealed with 18S rDNA metabarcoding. Coral Reefs 2020; 39:229.
  • F Ricci, VR Marcelino, LL Blackall, M Kühl, M Medina, H Verbruggen. Beneath the surface: community assembly and functions of the coral skeleton microbiome. Microbiome 2019; 7:159.
  • VR Marcelino*, L Irinyi, JS Eden, W Meyer, EC Holmes, TC Sorrell. Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions. IMA Fungus 2019; 10:8.
  • R Wetherbee, VR Marcelino, JF Costa, B Grant, S Crawford, RF Waller, RA Andersen, D Berry, GI McFadden, H Verbruggen. A new marine prasinophyte genus alternates between a flagellate and a dominant benthic stage with microrhizoids for adhesion. Journal of Phycology 2019; 55:1210–1225.
  • VR Marcelino*, M Wille, AC Hurt, D González-Acuña, M Klaassen, JS Eden, M Shi, JR Iredell, TC Sorrell, EC Holmes. Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biology 2019; 17:31.
  • C Biswas, VR Marcelino, S Van Hal, C Halliday, E Martinez, Q Wang, S Kidd, K Kennedy, D Marriott, CO Morrissey, I Arthur, K Weeks, MA Slavin, TC Sorrell, V Sintchenko, W Meyer, SC-A Chen. Whole genome sequencing of Australian Candida glabrata isolates reveals genetic diversity and novel sequence types. Frontiers in Microbiology 2018; 9:2946.
  • MC Oliveira, SI Repetti, C Iha, CJ Jackson, P Díaz-Tapia, KM Lubiana, V Cassano, JF Costa, MC Cremen, VR Marcelino, H Verbruggen. High-throughput sequencing for algal systematics. European Journal of Phycology 2018; 53:256–272.
  • CM Cremen, F Leliaert, VR Marcelino, H Verbruggen. Large diversity of nonstandard genes and dynamic evolution of chloroplast genomes in siphonous green algae (Bryopsidales, Chlorophyta). Genome Biology and Evolution 2018; 10:1048–1061.
  • VR Marcelino*, MJH van Oppen, H Verbruggen. Highly structured prokaryote communities exist within the skeleton of coral colonies. ISME Journal 2018; 12:300–303.
  • VR Marcelino*, KM Morrow, DG Bourne, MJH van Oppen, H Verbruggen. Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef. Molecular Ecology 2017; 26:5344–5357.
  • H Verbruggen, VR Marcelino, MD Guiry, CM Cremen, CJ Jackson. Phylogenetic position of the coral symbiont Ostreobium inferred from chloroplast genome data. Journal of Phycology 2017; 53:790–803.
  • VR Marcelino* and H Verbruggen. Reference datasets of tufA and UPA markers to identify algae in metabarcoding surveys. Data in Brief 2017; 11:273–276.
  • VR Marcelino* and H Verbruggen. Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae. Scientific Reports 2016; 6:31508.
  • VR Marcelino*, CM Cremen, CJ Jackson, AWD Larkum, H Verbruggen. Evolutionary dynamics of chloroplast genomes in low light: a case study of the endolithic green alga Ostreobium quekettii. Genome Biology and Evolution 2016; 8:2939–2951.
  • CM Cremen, JM Huisman, VR Marcelino, H Verbruggen. Taxonomic revision of Halimeda (Bryopsidales, Chlorophyta) in southwestern Australia. Australian Systematic Botany 2016; 29:41–54.
  • VR Marcelino* and H Verbruggen. Ecological niche models of invasive seaweeds. Journal of Phycology 2015; 51:606–620.
  • H Verbruggen, VR Marcelino, JF Costa. Evolutionary dynamics of algal traits and diversity. Perspectives in Phycology 2014; 1:53–60.
  • VR Marcelino, CFB Haddad, J Alexandrino. Geographic distribution and morphological variation of striped and nonstriped populations of the Brazilian Atlantic Forest treefrog Hypsiboas bischoffi (Anura: Hylidae). Journal of Herpetology 2009; 43:351–361.