Lab Publications

2022

• Brumfield KD, Raupp MJ, Haji D, Simon C, Graf J, Cooley JR, Janton ST, Meister RC, Huq A, Colwell RR, Hasan NA. 2022. Gut microbiome insights from 16S rRNA analysis of 17-year periodical cicadas (Hemiptera: Magicicada spp.) Broods II, VI, and X. Scientific reports 12(1):16967 PMC4021573
• Testerman T, Beka L, Reichley SR, King S, Welch TJ, Wiens GD, Graf J. 2022. A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility. FEMS microbiology ecology 98(10):
• Testerman T, Li Z, Galuppo B, Graf J, Santoro N. 2022. Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth. Hepatology communications 6(8):1962-1974 PMC8714082

2021

• Thees AV, Pietrosimone KM, Melchiorre CK, Marden JN, Graf J, Lynes MA, Maltz-Matyschsyk M. 2021. PmtA Regulates Pyocyanin Expression and Biofilm Formation in . Frontiers in microbiology 12:789765 PMC3325935
• Presley SJ, Graf J, Hassan AF, Sjodin AR, Willig MR. 2021. Effects of Host Species Identity and Diet on the Biodiversity of the Microbiota in Puerto Rican Bats. Current microbiology 78(9):3526-3540
• Testerman T, Reichley SR, King S, Graf J. 2021. Draft Genome Sequence of Aeromonas popoffii ID682, Isolated from a Natural Water Source in Idaho. Microbiology resource announcements 10(29):e0044521 PMC6522516
• Testerman T, Reichley SR, King S, Graf J. 2021. Draft Genome Sequence of Janthinobacterium lividum ID1246, Isolated from a Rainbow Trout Hatchery Biofilm. Microbiology resource announcements 10(28):e0044421 PMC6522516
• McClure EA, Nelson MC, Lin A, Graf J. 2021. : Old World Leech Gut Microbial Community Structure Conserved in a New World Leech. Applied and environmental microbiology 87(10): PMC208504
• Graf J, Ledala N, Caimano MJ, Jackson E, Gratalo D, Fasulo D, Driscoll MD, Coleman S, Matson AP. 2021. High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon. mBio 12(1): PMC7015180
• Kloub L, Gosselin S, Fullmer M, Graf J, Gogarten JP, Bansal MS. 2021. Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes. Molecular biology and evolution 38(6):2639-2659 PMC2667022
• Bridges CM, Nelson MC, Graf J, Gage DJ. 2021. Draft Genome Sequences of sp. Strains BGC7 and HGC4, Isolated from the Hindgut of a Lower Termite. Microbiology resource announcements 10(4): PMC6031026

2020

• Graf J, Nelson MC, Colston SM. 2020. Closed Genome Sequence of Aeromonas veronii Strain Hm21, an Isolate from the Medicinal Leech Hirudo verbana. Microbiology resource announcements 9(42): PMC4836430
• Monga Kravetz A, Testerman T, Galuppo B, Graf J, Pierpont B, Siebel S, Feinn R, Santoro N. 2020. Effect of Gut Microbiota and PNPLA3 rs738409 Variant on Nonalcoholic Fatty Liver Disease (NAFLD) in Obese Youth. The Journal of clinical endocrinology and metabolism 105(10):e3575-85 PMC2725325
• Lee J, d'Aigle J, Atadja L, Quaicoe V, Honarpisheh P, Ganesh BP, Hassan A, Graf J, Petrosino J, Putluri N, Zhu L, Durgan DJ, Bryan RM, McCullough. 2020. Gut Microbiota-Derived Short-Chain Fatty Acids Promote Poststroke Recovery in Aged Mice. Circulation research 127(4):453-465 PMC3769299
• Talagrand-Reboul E, Colston SM, Graf J, Lamy B, Jumas-Bilak E. 2020. Comparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas. Genome biology and evolution 12(5):535-552 PMC5013049

2019

• Rangel LT, Marden J, Colston S, Setubal JC, Graf J, Gogarten JP. 2019. Identification and characterization of putative Aeromonas spp. T3SS effectors. PloS one 14(6):e0214035 PMC6548356
• Jozwick AKS, LaPatra SE, Graf J, Welch TJ. 2019. Flagellar regulation mediated by the Rcs pathway is required for virulence in the fish pathogen Yersinia ruckeri. Fish & shellfish immunology 91:306-314
• Goldstein S, Beka L, Graf J, Klassen JL. 2019. Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing. BMC genomics 20(1):23 PMC6325685

2018

• Talagrand-Reboul E, Latif-Eugenín F, Beaz-Hidalgo R, Colston S, Figueras MJ, Graf J, Jumas-Bilak E, Lamy B. 2018. Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads. PLoS ONE 13(8):e0201428 (PMC6093642)
• Benjamino J, Beka L, Graf J. 2018. Microbiome Analyses for Toxicological Studies. Curr Protoc Toxicol :e53
• Beka L, Fullmer MS, Colston SM, Nelson MC, Talagrand-Reboul E, Walker P, Ford B, Whitaker IS, Lamy B, Gogarten JP, Graf J. 2018. Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients. mBio 9((4)): PMC6058295
• Adami AJ, Bracken SJ, Guernsey LA, Rafti E, Maas KR, Graf J, Matson AP, Thrall RS, Schramm CM. 2018. Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma. Pediatr. Res. 84(3):426-434 (PMC6258300)
• Gogarten JF, Davies TJ, Benjamino J, Gogarten JP, Graf J, Mielke A, Mundry R, Nelson MC, Wittig RM, Leendertz FH, Calvignac-Spencer S. 2018. Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d'Ivoire. ISME J 12(10):2559-2574 (PMC6154966)
• Benjamino J, Lincoln S, Srivastava R, Graf J. 2018. Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration. Microbiome 6((1)):86 PMC5944116
• Spychala MS, Venna VR, Jandzinski M, Doran SJ, Durgan DJ, Ganesh BP, Ajami NJ, Putluri N, Graf J, Bryan RM, McCullough LD. 2018. Age-related changes in the gut microbiota influence systemic inflammation and stroke outcome. Ann. Neurol. 84(1):23-36 (PMC6119509)
• Colston SM, Navarro A, Martinez-Murcia AJ, Graf J. 2018. Draft Genome Sequence of Aeromonas cavernicola sp. nov. DSM 24474, Isolated from a Cavern Brook in the Moravia Region of the Czech Republic. Genome announcements 6((15)): PMC5897817
• Colston SM, Navarro A, Martinez-Murcia AJ, Graf J. 2018. Draft Genome Sequence of Aeromonas lusitana sp. nov. Strain DSM 24905, Isolated from a Hot Spring in Vila-Real, Portugal. Genome announcements 6((15)): PMC5897795

2017

• Talagrand-Reboul E, Roger F, Kimper JL, Colston SM, Graf J, Latif-Eugenín F, Figueras MJ, Petit F, Marchandin H, Jumas-Bilak E, Lamy B. 2017. Delineation of Taxonomic Species within Complex of Species: and Related Species as a Test Case. Front Microbiol 8:621 (PMC5394120)
• Evenhuis JP, LaPatra SE, Graf J. 2017. Draft Genome Sequence of the Fish Pathogen Strain CSF-298-10. Genome Announc 5(15): (PMC5391422)
• Tricò D, Di Sessa A, Caprio S, Chalasani N, Liu W, Liang T, Graf J, Herzog RI, Johnson CD, Umano GR, Feldstein AE, Santoro N. 2017. Oxidized Derivatives of Linoleic Acid in Pediatric Metabolic Syndrome: Is Their Pathogenic Role Modulated by the Genetic Background and the Gut Microbiota? Antioxidants & redox signaling 30(2):241-250 PMC6277079
• Cong X, Judge M, Xu W, Diallo A, Janton S, Brownell EA, Maas K, Graf J. 2017. Influence of Feeding Type on Gut Microbiome Development in Hospitalized Preterm Infants. Nurs Res 66(2):123-133 (PMC5334772)

2016

• Jozwick AK, Graf J, Welch TJ. 2016. The flagellar master operon flhDC is a pleiotropic regulator involved in motility and virulence of the fish pathogen Yersinia ruckeri. J. Appl. Microbiol. :
• Goffredo M, Mass K, Parks EJ, Wagner DA, McClure EA, Graf J, Savoye M, Pierpont B, Cline G, Santoro N. 2016. Role of Gut Microbiota and Short Chain Fatty Acids in Modulating Energy Harvest and Fat Partitioning in Youth. J. Clin. Endocrinol. Metab. 101(11):4367-4376 (PMC5095239)
• Marden JN, McClure EA, Beka L, Graf J. 2016. Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential. Front Microbiol 7:1569 (PMC5061737)
• Nelson MC, Varney JS, Welch TJ, Graf J. 2016. Draft Genome Sequence of Lactococcus garvieae Strain PAQ102015-99, an Outbreak Strain Isolated from a Commercial Trout Farm in the Northwestern United States. Genome announcements 4((4)): PMC4974324
• Graf J. 2016. Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates. Annual review of microbiology 70:375-93
• Crapser J, Ritzel R, Verma R, Venna VR, Liu F, Chauhan A, Koellhoffer E, Patel A, Ricker A, Maas K, Graf J, McCullough LD. 2016. Ischemic stroke induces gut permeability and enhances bacterial translocation leading to sepsis in aged mice. Aging (Albany NY) 8(5):1049-63 (PMC4931853)
• Cong X, Xu W, Janton S, Henderson WA, Matson A, McGrath JM, Maas K, Graf J. 2016. Gut Microbiome Developmental Patterns in Early Life of Preterm Infants: Impacts of Feeding and Gender. PLoS ONE 11(4):e0152751 (PMC4844123)
• Benjamino J, Graf J. 2016. Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes. Front Microbiol 7:171 (PMC4756164)

2015

• Ott BM, Beka L, Graf J, Rio RV. 2015. Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings. Genome Announc 3(6): (PMC4683228)
• Mosser T, Talagrand-Reboul E, Colston SM, Graf J, Figueras MJ, Jumas-Bilak E, Lamy B. 2015. Exposure to pairs of Aeromonas strains enhances virulence in the Caenorhabditis elegans infection model. Front Microbiol 6:1218 (PMC4631986)
• Li YF, Shi J, Nelson MC, Chen PH, Graf J, Li Y, Yu Z. 2015. Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover. Bioresour. Technol. 200:744-52
• Maltz M, LeVarge BL, Graf J. 2015. Identification of iron and heme utilization genes in Aeromonas and their role in the colonization of the leech digestive tract. Front Microbiol 6:763 (PMC4516982)
• Cong X, Henderson WA, Graf J, McGrath JM. 2015. Early Life Experience and Gut Microbiome: The Brain-Gut-Microbiota Signaling System. Adv Neonatal Care 15(5):314-23; quiz E1-2 (PMC4583334)
• Li YF, Abraham C, Nelson MC, Chen PH, Graf J, Yu Z. 2015. Effect of organic loading on the microbiota in a temperature-phased anaerobic digestion (TPAD) system co-digesting dairy manure and waste whey. Appl. Microbiol. Biotechnol. 99(20):8777-92
• Nelson MC, Bomar L, Graf J. 2015. Complete Genome Sequence of the Novel Leech Symbiont Mucinivorans hirudinis M3T. Genome announcements 3((1)): PMC4319616
• Nelson MC, LaPatra SE, Welch TJ, Graf J. 2015. Complete Genome Sequence of Yersinia ruckeri Strain CSF007-82, Etiologic Agent of Red Mouth Disease in Salmonid Fish. Genome announcements 3((1)): PMC4319512
• Nelson MC, Bomar L, Maltz M, Graf J. 2015. Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech Hirudo verbana. Int. J. Syst. Evol. Microbiol. 65(Pt 3):990-995 (PMC4811647)

2014

• Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J. 2014. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. mBio 5(6):e02136 (PMC4251997)
• Li YF, Nelson MC, Chen PH, Graf J, Li Y, Yu Z. 2014. Comparison of the microbial communities in solid-state anaerobic digestion (SS-AD) reactors operated at mesophilic and thermophilic temperatures. Appl. Microbiol. Biotechnol. 99(2):969-80
• Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J. 2014. Metagenomic analysis of the medicinal leech gut microbiota. Front Microbiol 5:151 (PMC4029005)
• Yu R, Smets BF, Gan P, MacKay AA, Graf J. 2014. Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater - surface water interface. Can. J. Microbiol. 60(5):277-86
• Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. 2014. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS ONE 9(4):e94249 (PMC3983156)
• Whitaker IS, Maltz M, Siddall ME, Graf J. 2014. Characterization of the digestive tract microbiota of Hirudo orientalis (medicinal leech) and antibiotic resistance profile. Plast. Reconstr. Surg. 133(3):408e-418e

2013

• Bomar L, Stephens WZ, Nelson MC, Velle K, Guillemin K, Graf J. 2013. Draft Genome Sequence of Aeromonas veronii Hm21, a Symbiotic Isolate from the Medicinal Leech Digestive Tract. Genome Announc 1(5): (PMC3790095)

2012

• Nyholm SV, Graf J. 2012. Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nat. Rev. Microbiol. 10(12):815-27 (PMC3870473)
• Bomar L, Graf J. 2012. Investigation into the physiologies of Aeromonas veronii in vitro and inside the digestive tract of the medicinal leech using RNA-seq. Biol. Bull. 223(1):155-66 (PMC3732745)
• Nelson MC, Graf J. 2012. Bacterial symbioses of the medicinal leech Hirudo verbana. Gut Microbes 3(4):322-31 (PMC3463490)

2011

• Graf J. 2011. Shifting paradigm on Bacillus thuringiensis toxin and a natural model for Enterococcus faecalis septicemia. mBio 2(4): (PMC3157895)
• Whitaker IS, Josty IC, Hawkins S, Azzopardi E, Naderi N, Graf J, Damaris L, Lineaweaver WC, Kon M. 2011. Medicinal leeches and the microsurgeon: a four-year study, clinical series and risk benefit review. Microsurgery 31(4):281-7
• Bomar L, Maltz M, Colston S, Graf J. 2011. Directed culturing of microorganisms using metatranscriptomics. MBio 2(2):e00012-11 (PMC3069634)
• Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J. 2011. Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS ONE 6(2):e16751 (PMC3040217)
• Moore J. 2011. On Gouty Concretions or Chalk Stones. Med Chir Trans 1:112-22 (PMC2128806)

2010

• Maltz M, Graf J. 2010. The type II secretion system is essential for erythrocyte lysis and gut colonization by the leech digestive tract symbiont Aeromonas veronii. Applied and environmental microbiology 77(2):597-603 (PMC3020562)

2009

• Chopra AK, Graf J, Horneman AJ, Johnson JA. 2009. Virulence factor-activity relationships (VFAR) with specific emphasis on Aeromonas species (spp.). J Water Health 7 Suppl 1:S29-54
• Kikuchi Y, Bomar L, Graf J. 2009. Stratified bacterial community in the bladder of the medicinal leech, Hirudo verbana. Environ. Microbiol. 11(10):2758-70
• Rio RV, Maltz M, McCormick B, Reiss A, Graf J. 2009. Symbiont succession during embryonic development of the European medicinal leech, Hirudo verbana. Applied and environmental microbiology 75(21):6890-5 (PMC2772434)
• Silver AC, Graf J. 2009. Prevalence of genes encoding the type three secretion system and the effectors AexT and AexU in the Aeromonas veronii group. DNA Cell Biol. 28(8):383-8
• Whitaker IS, Kamya C, Azzopardi EA, Graf J, Kon M, Lineaweaver WC. 2009. Preventing infective complications following leech therapy: is practice keeping pace with current research? Microsurgery 29(8):619-25

2008

• Laufer AS, Siddall ME, Graf J. 2008. Characterization of the digestive-tract microbiota of Hirudo orientalis, a european medicinal leech. Appl. Environ. Microbiol. 74(19):6151-4 (PMC2565982)
• Yu R, Graf J, Smets BF. 2008. An improved cell recovery method for iron oxidizing bacterial (IOB) enrichments. J. Microbiol. Methods 72(3):235-40

2007

• Silver AC, Rabinowitz NM, Küffer S, Graf J. 2007. Identification of Aeromonas veronii genes required for colonization of the medicinal leech, Hirudo verbana. J. Bacteriol. 189(19):6763-72 (PMC2045196)
• Rio RV, Anderegg M, Graf J. 2007. Characterization of a catalase gene from Aeromonas veronii, the digestive-tract symbiont of the medicinal leech. Microbiology (Reading, Engl.) 153(Pt 6):1897-906
• Silver AC, Kikuchi Y, Fadl AA, Sha J, Chopra AK, Graf J. 2007. Interaction between innate immune cells and a bacterial type III secretion system in mutualistic and pathogenic associations. Proc. Natl. Acad. Sci. U.S.A. 104(22):9481-6 (PMC1890520)
• Kikuchi Y, Graf J. 2007. Spatial and temporal population dynamics of a naturally occurring two-species microbial community inside the digestive tract of the medicinal leech. Appl. Environ. Microbiol. 73(6):1984-91 (PMC1828818)
• Siddall ME, Worthen PL, Johnson M, Graf J. 2007. Novel role for Aeromonas jandaei as a digestive tract symbiont of the North American medicinal leech. Applied and environmental microbiology 73(2):655-8 (PMC1796983)

2006

• Seshadri R, Joseph SW, Chopra AK, Sha J, Shaw J, Graf J, Haft D, Wu M, Ren Q, Rosovitz MJ, Madupu R, Tallon L, Kim M, Jin S, Vuong H, Stine OC, Ali A,. 2006. Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades. J. Bacteriol. 188(23):8272-82 (PMC1698176)
• Graf J, Kikuchi Y, Rio RV. 2006. Leeches and their microbiota: naturally simple symbiosis models. Trends Microbiol. 14(8):365-71
• Worthen PL, Gode CJ, Graf J. 2006. Culture-independent characterization of the digestive-tract microbiota of the medicinal leech reveals a tripartite symbiosis. Applied and environmental microbiology 72(7):4775-81 (PMC1489327)
• Graf J. 2006. Molecular requirements for the colonization of Hirudo medicinalis by Aeromonas veronii. Prog. Mol. Subcell. Biol. 41:291-303

2005

• Morandi A, Zhaxybayeva O, Gogarten JP, Graf J. 2005. Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains. J. Bacteriol. 187(18):6561-4 (PMC1236645)

2003

• Braschler TR, Merino S, Tomas JM, Graf J. 2003. Complement resistance is essential for colonization of the digestive tract of Hirudo medicinalis by Aeromonas strains. Applied and environmental microbiology 69(7):4268-71 (PMC165153)