Hakimzadeh, A. ORCID: https://orcid.org/0000-0003-1336-7445, Abdala Asbun, A., Albanese, D., Bernard, M. ORCID: https://orcid.org/0000-0001-9005-5563, Buchner, D. ORCID: https://orcid.org/0000-0002-8499-5863, Callahan, B., Caporaso, J. G., Curd, E., Djemiel, C. ORCID: https://orcid.org/0000-0002-5659-7876, Brandström Durling, M. ORCID: https://orcid.org/0000-0001-6485-197X, Elbrecht, V. ORCID: https://orcid.org/0000-0003-4672-7099, Gold, Z., Gweon, S. ORCID: https://orcid.org/0000-0002-6218-6301, Hajibabaei, M. ORCID: https://orcid.org/0000-0002-8859-7977, Hildebrand, F., Mikryukov, V., Normandeau, E., Özkurt, E., M. Palmer, J., Pascal, G. ORCID: https://orcid.org/0000-0002-5250-6594, Porter, T. M., Straub, D., Vasar, M. ORCID: https://orcid.org/0000-0002-4674-932X, Větrovský, T., Zafeiropoulos, H. and Anslan, S. ORCID: https://orcid.org/0000-0002-2299-454X (2023) A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Molecular Ecology Resources. ISSN 1755-0998 doi: https://doi.org/10.1111/1755-0998.13847

Yokoyama, M., Peto, L., Budgell, E. P. ORCID: https://orcid.org/0000-0002-6148-9378, Jones, N., Sheridan, E., Liu, J., Walker, A. S., Stoesser, N., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 and Llewelyn, M. J. (2023) Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing. PLOS ONE, 18 (3). e0282584. ISSN 1932-6203 doi: https://doi.org/10.1371/journal.pone.0282584

Withey, Z. ORCID: https://orcid.org/0000-0001-5031-4815, Awan, A., Duguma, N., Fell, E., Martinez, N. J., Neary, E., Goodall, T. and Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 (2023) Mycobial community assemblages in sink drains across a university campus. Environmental DNA, 5 (1). pp. 212-224. ISSN 2637-4943 doi: https://doi.org/10.1002/edn3.375

Thorpe, A. C. ORCID: https://orcid.org/0000-0003-0210-2767, Anderson, A., Goodall, T., Thackeray, S. J., Maberly, S. C., Bendle, J. A., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 and Read, D. S. ORCID: https://orcid.org/0000-0001-8546-5154 (2022) Sedimentary DNA records long‐term changes in a lake bacterial community in response to varying nutrient availability. Environmental DNA, 4 (6). pp. 1340-1355. ISSN 2637-4943 doi: https://doi.org/10.1002/edn3.344

Mombrikotb, S. B., Van Agtmaal, M., Johnstone, E., Crawley, M. J., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Griffiths, R. I. ORCID: https://orcid.org/0000-0002-3341-4547 and Bell, T. ORCID: https://orcid.org/0000-0002-2615-3932 (2022) The interactions and hierarchical effects of long-term agricultural stressors on soil bacterial communities. Environmental Microbiology Reports, 14 (5). pp. 711-718. ISSN 1758-2229 doi: https://doi.org/10.1111/1758-2229.13106

Palacio-Cortés, A. M., Horton, A. A., Newbold, L., Spurgeon, D., Lahive, E., Pereira, M. G., Grassi, M. T., Moura, M. O., Disner, G. R., Cestari, M. M., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 and Navarro-Silva, M. A. (2022) Accumulation of nylon microplastics and polybrominated diphenyl ethers and effects on gut microbial community of Chironomus sancticaroli. Science of the Total Environment, 832. 155089. ISSN 0048-9697 doi: https://doi.org/10.1016/j.scitotenv.2022.155089

Woodcock, B. A., Oliver, A. E., Newbold, L. K., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Read, D. S., Sayed, U., Savage, J., Bacon, J., Upcott, E., Howell, K., Turvey, K., Roy, D. B., Gloria Pereira, M., Sleep, D., Greenop, A. and Pywell, R. F. (2022) Citizen science monitoring reveals links between honeybee health, pesticide exposure and seasonal availability of floral resources. Scientific Reports, 12 (1). 14331. ISSN 2045-2322 doi: https://doi.org/10.1038/s41598-022-18672-0

Schönrogge, K. ORCID: https://orcid.org/0000-0003-0122-6493, Gibbs, M., Oliver, A., Cavers, S., Gweon, H.S. ORCID: https://orcid.org/0000-0002-6218-6301, Ennos, R.A., Cottrell, J., Iason, G.R. and Taylor, J. (2022) Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris). Fungal Ecology, 57-58. 101162. ISSN 17545048 doi: https://doi.org/10.1016/j.funeco.2022.101162

Oliveira, J. M. M., Henriques, I., Read, D. S., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Morgado, R. G., Peixoto, S., Correia, A., Soares, A. M. V. M. and Loureiro, S. (2021) Gut and faecal bacterial community of the terrestrial isopod Porcellionides pruinosus: potential use for monitoring exposure scenarios. Ecotoxicology, 30. pp. 2096-2108. ISSN 0963-9292 doi: https://doi.org/10.1007/s10646-021-02477-4

McGorum, B. C. ORCID: https://orcid.org/0000-0002-6977-6101, Chen, Z., Glendinning, L., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Hunt, L., Ivens, A., Keen, J. A., Pirie, R. S., Taylor, J., Wilkinson, T. and McLachlan, G. (2021) Equine grass sickness (a multiple systems neuropathy) is associated with alterations in the gastrointestinal mycobiome. Animal Microbiome, 3 (70). ISSN 2524-4671 doi: https://doi.org/10.1186/s42523-021-00131-2

Rivett, D. W., Mombrikotb, S. B., Gweon, H. ORCID: https://orcid.org/0000-0002-6218-6301, Bell, T. and van der Gast, C. (2021) Bacterial communities in larger islands have reduced temporal turnover. ISME Journal, 15. pp. 2947-2955. ISSN 1751-7370 doi: https://doi.org/10.1038/s41396-021-00976-0

Withey, Z., Goodall, T., MacIntyre, S. and Gweon, S. ORCID: https://orcid.org/0000-0002-6218-6301 (2021) Characterization of communal sink drain communities of a university campus. Environmental DNA, 3 (5). ISSN 2637-4943 doi: https://doi.org/10.1002/edn3.196

Matlock, W. ORCID: https://orcid.org/0000-0001-5608-0423, Chau, K. K., AbuOun, M., Stubberfield, E., Barker, L., Kavanagh, J., Pickford, H., Gilson, D., Smith, R. P., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Hoosdally, S. J., Swann, J., Sebra, R., Bailey, M. J., Peto, T. E. A., Crook, D. W., Anjum, M. F., Read, D. S., Walker, A. S., Stoesser, N. and Shaw, L. P. (2021) Genomic network analysis of environmental and livestock F-type plasmid populations. The ISME Journal, 15. pp. 2322-2335. ISSN 1751-7370 doi: https://doi.org/10.1038/s41396-021-00926-w

Jones, B., Goodall, T., George, P. B. L., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Puissant, J., Read, D. S., Emmett, B. A., Robinson, D. A., Jones, D. L. and Griffiths, R. I. (2021) Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database. Frontiers in Microbiology, 12. ISSN 1664-302X doi: https://doi.org/10.3389/fmicb.2021.682886

Shaw, L. P. ORCID: https://orcid.org/0000-0001-7332-0820, Chau, K. K. ORCID: https://orcid.org/0000-0002-6926-080X, Kavanagh, J. ORCID: https://orcid.org/0000-0003-1495-0843, AbuOun, M. ORCID: https://orcid.org/0000-0003-4190-1473, Stubberfield, E. ORCID: https://orcid.org/0000-0002-5527-1209, Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Barker, L., Rodger, G. ORCID: https://orcid.org/0000-0001-6051-8985, Bowes, M. J. ORCID: https://orcid.org/0000-0002-0673-1934, Hubbard, A. T. M., Pickford, H., Swann, J. ORCID: https://orcid.org/0000-0002-1475-8248, Gilson, D. ORCID: https://orcid.org/0000-0002-3713-1966, Smith, R. P., Hoosdally, S. J., Sebra, R., Brett, H. ORCID: https://orcid.org/0000-0002-4100-8565, Peto, T. E. A., Bailey, M. J., Crook, D. W. ORCID: https://orcid.org/0000-0002-0590-2850, Read, D. S. ORCID: https://orcid.org/0000-0001-8546-5154, Anjum, M. F., Walker, A. S. ORCID: https://orcid.org/0000-0002-0412-8509 and Stoesser, N. ORCID: https://orcid.org/0000-0002-4508-7969 (2021) Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. Science Advances, 7 (15). eabe3868. ISSN 2375-2548 doi: https://doi.org/10.1126/sciadv.abe3868

Woodcock, B. A., Ridding, L., Pereira, M. G., Sleep, D., Newbold, L., Oliver, A., Shore, R. F., Bullock, J. M., Heard, M. S., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 and Pywell, R. F. (2021) Neonicotinoid use on cereals and sugar beet is linked to continued low exposure risk in honeybees. Agriculture Ecosystems & Environment, 308. 107205. ISSN 0167-8809 doi: https://doi.org/10.1016/j.agee.2020.107205

Merino-Martín, L., Stokes, A., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Moragues-Saitua, L., Staunton, S., Plassard, C., Oliver, A., Le Bissonnais, Y. and Griffiths, R. I. (2021) Interacting effects of land use type, soil microbes and plant traits on aggregate stability. Soil Biology & Biochemistry, 154. 108072. ISSN 0038-0717 doi: https://doi.org/10.1016/j.soilbio.2020.108072

Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Bowes, M. J., Moorhouse, H. L., Oliver, A. E., Bailey, M. J., Acreman, M. C. and Read, D. S. ORCID: https://orcid.org/0000-0001-8546-5154 (2021) Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum. Environmental Microbiology, 23 (1). pp. 484-498. ISSN 1462-2912 doi: https://doi.org/10.1111/1462-2920.15337

Oliver, A. E. ORCID: https://orcid.org/0000-0003-4923-277X, Newbold, L. K. ORCID: https://orcid.org/0000-0001-8895-1406, Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Read, D. S., Woodcock, B. A. ORCID: https://orcid.org/0000-0003-0300-9951 and Pywell, R. F. (2021) Integration of DNA extraction, metabarcoding and an informatics pipeline to underpin a national citizen science honey monitoring scheme. MethodsX, 8. 101303. ISSN 22150161 doi: https://doi.org/10.1016/j.mex.2021.101303

AbuOun, M., Jones, H., Stubberfield, E., Gilson, D., Shaw, L., Hubbard, A., Chau, K., Sebra, R., Peto, T., Crook, D., Read, D., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Walker, S., Stoesser, N., Smith, R. and Anjum, M. (2021) A genomic epidemiological study shows prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage. Microbial Genomics, 7 (10). 000630. ISSN 2057-5858 doi: https://doi.org/10.1099/mgen.0.000630

Constantinides, B., Chau, K. K., Quan, T. P., Rodger, G., Andersson, M. I., Jeffery, K., Lipworth, S., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Peniket, A., Pike, G., Millo, J., Byukusenge, M., Holdaway, M., Gibbons, C., Mathers, A. J., Crook, D. W., Peto, T. E. A., Walker, A. S. and Stoesser, N. (2020) Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microbial Genomics, 6 (7). ISSN 2057-5858 doi: https://doi.org/10.1099/mgen.0.000391

Kotay, S. M., Parikh, H. I., Barry, K., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Guilford, W., Carroll, J. and Mathers, A. J. (2020) Nutrients influence the dynamics of Klebsiella pneumoniae carbapenemase producing enterobacterales in transplanted hospital sinks. Water Research, 176. 115707. ISSN 0043-1354 doi: https://doi.org/10.1016/j.watres.2020.115707

Merino-Martín, L., Griffiths, R. I., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Furget-Bretagnon, C., Oliver, A., Mao, Z., Le Bissonnais, Y. and Stokes, A. (2020) Rhizosphere bacteria are more strongly related to plant root traits than fungi in temperate montane forests: insights from closed and open forest patches along an elevational gradient. Plant and Soil, 450 (1-2). pp. 183-200. ISSN 0032-079X doi: https://doi.org/10.1007/s11104-020-04479-3

Horton, A. A., Newbold, L. K., Palacio-Cortés, A. M., Spurgeon, D. J., Pereira, M. G., Carter, H., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Vijver, M. G., van Bodegom, P. M., Navarro da Silva, M. A. and Lahive, E. (2020) Accumulation of polybrominated diphenyl ethers and microbiome response in the great pond snail Lymnaea stagnalis with exposure to nylon (polyamide) microplastics. Ecotoxicology and Environmental Safety, 188. 109882. ISSN 0147-6513 doi: https://doi.org/10.1016/j.ecoenv.2019.109882

Newbold, L. K., Robinson, A., Rasnaca, I., Lahive, E., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Lapied, E., Oughton, D., Gashchak, S., Beresford, N. A. and Spurgeon, D. J. (2019) Genetic, epigenetic and microbiome characterisation of an earthworm species (Octolasion lacteum) along a radiation exposure gradient at Chernobyl. Environmental Pollution, 255 (Part 1). 113238. ISSN 0269-7491 doi: https://doi.org/10.1016/j.envpol.2019.113238

Puissant, J., Jones, B., Goodall, T., Mang, D., Blaud, A., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Malik, A., Jones, D. L., Clark, I. M., Hirsch, P. R. and Griffiths, R. (2019) The pH optimum of soil exoenzymes adapt to long term changes in soil pH. Soil Biology and Biochemistry, 138. 107601. ISSN 0038-0717 doi: https://doi.org/10.1016/j.soilbio.2019.107601

Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Shaw, L. P., Swann, J., De Maio, N., AbuOun, M., Niehus, R., Hubbard, A. T. M., Bowes, M. J., Bailey, M. J., Peto, T. E. A., Hoosdally, S. J., Walker, A. S., Sebra, R. P., Crook, D. W., Anjum, M. F., Read, D. S., Stoesser, N. and REHAB Consortium, (2019) The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. Environmental Microbiome, 14 (1). 7. ISSN 2524-6372 doi: https://doi.org/10.1186/s40793-019-0347-1

Malik, A. A., Puissant, J., Buckeridge, K. M., Goodall, T., Jehmlich, N., Chowdhury, S., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Peyton, J. M., Mason, K. E., van Agtmaal, M., Blaud, A., Clark, I. M., Whitaker, J., Pywell, R. F., Ostle, N., Gleixner, G. and Griffiths, R. I. (2018) Land use driven change in soil pH affects microbial carbon cycling processes. Nature Communications, 9 (1). 3591. ISSN 2041-1723 doi: https://doi.org/10.1038/s41467-018-05980-1

de Vries, F. T., Griffiths, R. I., Bailey, M., Craig, H., Girlanda, M., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Hallin, S., Kaisermann, A., Keith, A. M., Kretzschmar, M., Lemanceau, P., Lumini, E., Mason, K. E., Oliver, A., Ostle, N., Prosser, J. I., Thion, C., Thomson, B. and Bardgett, R. D. (2018) Soil bacterial networks are less stable under drought than fungal networks. Nature communications, 9 (1). 3033. ISSN 2041-1723 doi: https://doi.org/10.1038/s41467-018-05516-7

van der Linde, S., Suz, L. M., Orme, C. D. L., Cox, F., Andreae, H., Asi, E., Atkinson, B., Benham, S., Carroll, C., Cools, N., De Vos, B., Dietrich, H.-P., Eichhorn, J., Gehrmann, J., Grebenc, T., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Hansen, K., Jacob, F., Kristöfel, F., Lech, P., Manninger, M., Martin, J., Meesenburg, H., Merilä, P., Nicolas, M., Pavlenda, P., Rautio, P., Schaub, M., Schröck, H.-W., Seidling, W., Šrámek, V., Thimonier, A., Thomsen, I. M., Titeux, H., Vanguelova, E., Verstraeten, A., Vesterdal, L., Waldner, P., Wijk, S., Zhang, Y., Žlindra, D. and Bidartondo, M. I. (2018) Environment and host as large-scale controls of ectomycorrhizal fungi. Nature, 558. pp. 243-248. ISSN 0028-0836 doi: https://doi.org/10.1038/s41586-018-0189-9

Durand, A., Maillard, F., Foulon, J., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Valot, B. and Chalot, M. (2017) Environmental metabarcoding reveals contrasting belowground and aboveground fungal communities from poplar at a Hg phytomanagement site. Microbial Ecology, 74 (4). pp. 795-809. ISSN 1432-184X doi: https://doi.org/10.1007/s00248-017-0984-0

Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Bailey, M. J. and Read, D. S. (2017) Assessment of the bimodality in the distribution of bacterial genome sizes. The ISME Journal, 11 (3). pp. 821-824. ISSN 1751-7370 doi: https://doi.org/10.1038/ismej.2016.142

Newbold, L. K., Burthe, S. J., Oliver, A. E., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Barnes, C. J., Daunt, F. and van der Gast, C. J. (2017) Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota. The ISME Journal, 11 (3). pp. 663-675. ISSN 1751-7370 doi: https://doi.org/10.1038/ismej.2016.153

Read, D. S., Matzke, M., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Newbold, L., Heggelund, L., Ortiz, M. D., Lahive, E., Spurgeon, D. and Svendsen, C. (2016) Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities. Environmental Science and Pollution Research, 23 (5). pp. 4120-4128. ISSN 1614-7499 doi: https://doi.org/10.1007/s11356-015-4538-z

Griffiths, R. I., Thomson, B. C., Plassart, P., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Stone, D., Creamer, R. E., Lemanceau, P. and Bailey, M. J. (2016) Mapping and validating predictions of soil bacterial biodiversity using European and national scale datasets. Applied Soil Ecology, 97. p. 61. ISSN 0929-1393 doi: https://doi.org/10.1016/j.apsoil.2015.06.018

Day, J. C., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 and Post, R. J. (2016) Sequence and organization of the complete mitochondrial genome of the blackfly Simulium variegatum (Diptera: Simuliidae). Mitochondrial DNA Part B, 1 (1). pp. 799-801. ISSN 2380-2359 doi: https://doi.org/10.1080/23802359.2016.1209091

Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., Griffiths, R. I. and Schonrogge, K. (2015) PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods in Ecology and Evolution, 6 (8). pp. 973-980. ISSN 2041-210X doi: https://doi.org/10.1111/2041-210X.12399

Newbold, L. K., Oliver, A. E., Cuthbertson, L., Walkington, S. E., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Heard, M. S. and van der Gast, C. J. (2015) Rearing and foraging affects bumblebee (Bombus terrestris) gut microbiota. Environmental Microbiology Reports, 7 (4). pp. 634-641. ISSN 1758-2229 doi: https://doi.org/10.1111/1758-2229.12299

Read, D. S., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Bowes, M. J., Newbold, L. K., Field, D., Bailey, M. J. and Griffiths, R. I. (2014) Catchment-scale biogeography of riverine bacterioplankton. The ISME Journal, 9 (2). pp. 516-526. ISSN 1751-7370 doi: https://doi.org/10.1038/ismej.2014.166

Booth, T., Bicak, M., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301 and Field, D. (2012) Bio-Linux as a tool for bioinformatics training. IEEE. doi: https://doi.org/10.1109/BIBE.2012.6399736

Ottenhof, H. H., Ashurst, J. L., Whitney, H. M., Saldanha, S. A., Schmitzberger, F., Gweon, H. S. ORCID: https://orcid.org/0000-0002-6218-6301, Blundell, T. L., Abell, C. and Smith, A. G. (2003) Organisation of the pantothenate (vitamin B5) biosynthesispathway in higher plants. The Plant Journal, 37 (1). pp. 61-72. ISSN 0960-7412 doi: https://doi.org/10.1046/j.1365-313X.2003.01940.x