NU-OMICS Journals

NU-OMICS Publications

2020

• Acquisition and Development of the Extremely Preterm Infant Microbiota across Multiple Anatomical Sites. (2020) Young GR, van der Gast CJ, Smith DL, Berrington JE, Embleton ND, Lanyon C. J Pediatr Gastroenterol Nutr. 70(1):12-19. doi: 10.1097/MPG.0000000000002549.

2019

• Temperate Bacteriophages from Chronic Pseudomonas aeruginosa Lung Infections Show Disease-Specific Changes in Host Range and Modulate Antimicrobial Susceptibility. (2019) Tariq MA, Everest FLC, Cowley LA, Wright R, Holt GS, Ingram H, Duignan LAM, Nelson A, Lanyon CV, Perry A, Perry JD, Bourke S, Brockhurst MA, Bridge SH, De Soyza A, Smith DL. mSystems. 4;4(4). pii: e00191-18. doi: 10.1128/mSystems.00191-18.

• Microbiome acquisition during larval settlement of the barnacle Semibalanus balanoides. (2019) Aldred N, Nelson A. Biol Lett. 28;15(6):20180763. doi: 10.1098/rsbl.2018.0763.

• Mucosal lactoferrin response to genital tract infections is associated with iron and nutritional biomarkers in young Burkinabé women. (2019) Roberts SA, Brabin L, Diallo S, Gies S, Nelson A, Stewart C, Swinkels DW, Geurts-Moespot AJ, Kazienga A, Ouedraogo S, D'Alessandro, Tinto H, Brabin BJ. Eur J Clin Nutr. 73(11):1464-1472. doi: 10.1038/s41430-019-0444-7.

• Mycolicibacterium stellerae sp. nov., a rapidly growing scotochromogenic strain isolated from Stellera chamaejasme. (2019) Nouioui I, Sangal V, Cortés-Albayay C, Jando M, Igual JM, Klenk HP, Zhang YQ, Goodfellow M. Int J Syst Evol Microbiol. 69(11):3465-3471. doi: 10.1099/ijsem.0.003644.

• Genomic analysis of a novel nontoxigenic Corynebacterium diphtheriae strain isolated from a cancer patient. (2019) Ramdhan ND, Blom J, Sutcliffe IC, Pereira-Ribeiro PMA, Santos CS, Mattos-Guaraldi AL, Burkovski A, Sangal V. New Microbes New Infect. 9;30:100544. doi: 10.1016/j.nmni.2019.100544.

• Biogeographical patterns in soil bacterial communities across the Arctic region. (2019) Malard LA, Anwar MZ, Jacobsen CS, Pearce DA. FEMS Microbiol Ecol. 1;95(9). pii: fiz128. doi: 10.1093/femsec/fiz128.

• Non-sterile heterotrophic cultivation of native wastewater yeast and microalgae for integrated municipal wastewater treatment and bioethanol production. (2019) Walls LE, Velasquez-Orta SB, Romero-Frasca E, Leary P, Noguez IY, Ledesma MTO. Biochemical Engineering Journal 151: 1073192. doi: 10.1016/j.bej.2019.107319.

• A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality. (2019) Acharya K, Khanal S, Pantha K, Amatya N, Davenport RJ, Werner D. Sci Rep. 31;9(1):15726. doi: 10.1038/s41598-019-51997-x.

• Reviving Phage Therapy for the Treatment of Cholera. (2019) Bhandare S, Colom J, Baig A, Ritchie JM, Bukhari H, Shah MA, Sarkar BL, Su J, Wren B, Barrow P, Atterbury RJ. J Infect Dis. 15;219(5):786-794. doi: 10.1093/infdis/jiy563.

2018

• Carbon amendment stimulates benthic nitrogen cycling during the bioremediation of particulate aquaculture waste. (2018) Robinson G, MacTavish T, Savage C, Caldwell GS, Jones CLW, Probyn T, Eyre BD, and Stead SM. Biogeosciences, 15:1863–1878. doi: 10.5194/bg-15-1863-2018.

• Links between bacteria derived from penguin guts and deposited guano and the surrounding soil microbiota. (2018) Yew WC, Pearce DA, Dunn MJ, Adlard S, Alias SA, Samah AA, Convey P. Polar Biol 41: 269. https://doi.org/10.1007/s00300-017-2189-x.

• Revisiting the taxonomic status of the biomedically and industrially important genus Amycolatopsis, using a phylogenomic approach. (2018) Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk HP, Sutcliffe IC. Front Microbiol. 9:2281.

• The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens. (2018) Connerton PL, Richards PJ, Lafontaine GM, O'Kane PM, Ghaffar N, Cummings NJ, Smith DL, Fish NM, Connerton IF. Microbiome. 12;6(1):88. doi: 10.1186/s40168-018-0477-5.

• Genomic analyses reveal two distinct lineages of Corynebacterium ulcerans strains. (2018) Subedi R, Kolodkina V, Sutcliffe IC, Simpson-Louredo L, Hirata R Jr, Titov L, Mattos-Guaraldi AL, Burkovski A, Sangal V. New Microbes New Infect. 25:7-13.

• Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert. (2018) Castro JF, Nouioui I, Sangal V, Choi S, Yang SJ, Kim BY, Trujillo ME, Riesco R, Montero-Calasanz MDC, Rahmani TPD, Bull AT, Sutcliffe IC, Asenjo JA, Andrews B, Goodfellow M.  Int J Syst Evol Microbiol. 68(9):2712-2721.

• The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection. (2018) Cullen L, O'Connor A, McCormack S, Owens RA, Holt GS, Collins C, Callaghan M, Doyle S, Smith D, Schaffer K, Fitzpatrick DA, McClean S. Sci Rep. 6;8(1):13386. doi: 10.1038/s41598-018-31556-6.

• Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC, Rahmani T, Bull AT, Asenjo JA, Andrews BA, Goodfellow M. (2018) Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile. Syst Appl Microbiol. S0723-2020(18)30129-2.

• Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution. (2018) Augustyniak D, Seredyński R, McClean S, Roszkowiak J, Roszniowski B, Smith DL, Drulis-Kawa Z, Mackiewicz P. Sci Rep. 21;8(1):4955. doi: 10.1038/s41598-018-23029-7.

• Formal description of Mycobacterium neglectum sp. nov. and Mycobacterium palauense sp. nov., rapidly growing actinobacteria. (2018) Nouioui I, Carro L, Sangal V, Jando M, Igual JM, Goodfellow M, Klenk HP. Antonie Van Leeuwenhoek. 111(7):1209-1223.

• Excess Mucin Impairs Subglottic Epithelial Host Defense in Mechanically Ventilated Patients. Powell J, Garnett J, Mather MW, Cooles FAH, Nelson A, Verdon B, Scott J, Jiwa K, Ruchaud-Sparagano MH, Cummings SP, Perry JD, Wright SE, Wilson JA, Pearson J, Ward C, Simpson AJ. (2018) Am J Respir Crit Care Med. doi: 10.1164/rccm.201709-1819OC

2017

• Effects of long-term weekly iron and folic acid supplementation on lower genital tract infection - a double blind, randomised controlled trial in Burkina Faso. (2017) Brabin L, Roberts SA, Gies S, Nelson A, Diallo S, Stewart CJ, Kazienga A, Birtles J, Ouedraogo S, Claeys Y, Tinto H, d'Alessandro U, Faragher EB, Brabin B. BMC Med. doi: 10.1186/s12916-017-0967-5.

• Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s. (2017) Grosse-Kock S, Kolodkina V, Schwalbe EC, Blom J, Burkovski A, Hoskisson PA, Brisse S, Smith D, Sutcliffe IC, Titov L, Sangal V. BMC Genomics. 13;18(1):873. doi: 10.1186/s12864-017-4276-3.

• Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection. (2017) Baig A, Colom J, Barrow P, Schouler C, Moodley A, Lavigne R, Atterbury R. Front Microbiol. 30;8:1652. doi: 10.3389/fmicb.2017.01652.

• Two novel species of rapidly growing mycobacteria: Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov. (2017) Nouioui I, Sangal V, Carro L, Teramoto K, Jando M, Montero-Calasanz MDC, Igual JM, Sutcliffe I, Goodfellow M, Klenk HP. Int J Syst Evol Microbiol. 67(12):4948-4955.

• Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. (2017) Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, Skeath T, Perry JD, Petrosino JF, Berrington JE, Cummings SP. Microbiome. doi: 10.1186/s40168-017-0295-1.

• A comparative in situ decomposition study using stillborn piglets and leaf litter from a deciduous forest. (2017) Olakanye AO, Nelson A, Ralebitso-Senior TK. Forensic Sci Int. doi: 10.1016/j.forsciint.2017.04.024.

• Reducing viability bias in analysis of gut microbiota in preterm infants at risk of NEC and sepsis. (2017) Young GR, Smith DL, Embleton ND, Berrington JE, Schwalbe EC, Cummings SP, van der Gast CJ, Lanyon C. Front Cell Infect Microbiol. 6;7:237. doi: 10.3389/fcimb.2017.00237.

• Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum. (2017) Nouioui I, Carro L, Teramoto K, Igual JM, Jando M, Del Carmen Montero-Calasanz M, Sutcliffe I, Sangal V, Goodfellow M, Klenk HP. Int J Syst Evol Microbiol. 67(9):3174-3181.

• Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. (2017) Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Front Microbiol. 6;8:1008. doi: 10.3389/fmicb.2017.01008. eCollection 2017.

• The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage. (2017) Roszniowski B, Latka A, Maciejewska B, Vandenheuvel D, Olszak T, Briers Y, Holt GS, Valvano MA, Lavigne R, Smith DL, Drulis-Kawa Z. Appl Microbiol Biotechnol. 101(3):1203-1216. doi: 10.1007/s00253-016-7924-7.

• Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe. (2017) Fogg PC, Haley JA, Stark WM, Smith MC. Appl Environ Microbiol. 15;83(5). pii: e02767-16. doi: 10.1128/AEM.02767-16.

• Gut microbiota of Type 1 diabetes patients with good glycaemic control and high physical fitness is similar to people without diabetes: an observational study. (2017) Stewart CJ, Nelson A, Campbell MD, Walker M, Stevenson EJ, Shaw JA, Cummings SP, West DJ. Diabet Med. 34(1):127-134. doi: 10.1111/dme.13140.

• Shigatoxin encoding Bacteriophage ϕ24B modulates bacterial metabolism to raise antimicrobial tolerance. (2017) Holt GS, Lodge JK, McCarthy AJ, Graham AK, Young G, Bridge SH, Brown AK, Veses-Garcia M, Lanyon CV, Sails A, Allison HE, Smith DL. Sci Rep. 20;7:40424. doi: 10.1038/srep40424.

2016

• Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. (2016) Stewart CJ, Embleton ND, Marrs EC, Smith DP, Nelson A, Abdulkadir B, Skeath T, Petrosino JF, Perry JD, Berrington JE, Cummings SP. Microbiome. 29;4(1):67. doi: 10.1186/s40168-016-0216-8.

• Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF. (2016) Leon-Velarde CG, Happonen L, Pajunen M, Leskinen K, Kropinski AM, Mattinen L, Rajtor M, Zur J, Smith D, Chen S, Nawaz A, Johnson RP, Odumeru JA, Griffiths MW, Skurnik M. Appl Environ Microbiol. 15;82(17):5340-53. doi: 10.1128/AEM.01594-16.

• Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa. (2016) Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J, Hoskisson PA, Sutcliffe IC. Sci Rep. 6:38392.

• Functional changes in gut microbiota during hematopoietic stem cell transplantation for severe combined immunodeficiency. (2016) Lane JP, Stewart CJ, Cummings SP, Gennery AR. J Allergy Clin Immunol. 138(2):622-625.e3. doi: 10.1016/j.jaci.2016.02.019.

• Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients. (2016) Al-Momani H, Perry A, Stewart CJ, Jones R, Krishnan A, Robertson AG, Bourke S, Doe S, Cummings SP, Anderson A, Forrest T, Griffin SM, Brodlie M, Pearson J, Ward C. Sci Rep. 1;6:26985. doi: 10.1038/srep26985.

• Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome. (2016) Abdulkadir B, Nelson A, Skeath T, Marrs EC, Perry JD, Cummings SP, Embleton ND, Berrington JE, Stewart CJ. Neonatology. 109(4):239-47. doi: 10.1159/000442936.

2015

• Preterm gut microbiota and metabolome following discharge from intensive care. (2015) Stewart CJ, Skeath T, Nelson A, Fernstad SJ, Marrs EC, Perry JD, Cummings SP, Berrington JE, Embleton ND. Sci Rep. 24;5:17141. doi: 10.1038/srep17141.

• A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients. (2015) Tariq MA, Everest FL, Cowley LA, De Soyza A, Holt GS, Bridge SH, Perry A, Perry JD, Bourke SJ, Cummings SP, Lanyon CV, Barr JJ, Smith DL. Front Microbiol. 18;6:97. doi: 10.3389/fmicb.2015.00097. 

• Gut microbiome variations during hematopoietic stem cell transplant in severe combined immunodeficiency. (2015) Lane JP, Stewart CJ, Cummings SP, Gennery AR. J Allergy Clin Immunol. 135(6):1654-6. doi: 10.1016/j.jaci.2015.01.024.