MacDonald TT, Monteleone G. Immunity, inflammation, and allergy in the gut. Science. 2005;307:1920.
Article
CAS
PubMed
Google Scholar
Tremaroli V, Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489:242.
Article
CAS
PubMed
Google Scholar
Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015;26:26191.
PubMed
Google Scholar
Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17:219–32.
Article
CAS
PubMed
Google Scholar
Stubbendieck RM, Straight PD. Multifaceted interfaces of bacterial competition. J Bacteriol. 2016;198:2145.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stubbendieck RM, Vargas-Bautista C, Straight PD. Bacterial communities: interactions to scale. Front Microbiol. 2016;7:1234.
Article
PubMed
PubMed Central
Google Scholar
Becker N, Kunath J, Loh G, Blaut M. Human intestinal microbiota: characterization of a simplified and stable gnotobiotic rat model. Gut Microbes. 2011;2:25–33.
Article
PubMed
Google Scholar
Krause JL, Schaepe SS, Fritz-Wallace K, Engelmann B, Rolle-Kampczyk U, Kleinsteuber S, Schattenberg F, Liu Z, Mueller S, Jehmlich N, et al. Following the community development of SIHUMIx – a new intestinal in vitro model for bioreactor use. Gut Microbes. 2020;11(4):1–14. https://doi.org/10.1080/19490976.2019.1702431.
Schäpe SS, Krause JL, Engelmann B, Fritz-Wallace K, Schattenberg F, Liu Z, Müller S, Jehmlich N, Rolle-Kampczyk U, Herberth G, von Bergen M. The simplified human intestinal microbiota (SIHUMIx) shows high structural and functional resistance against changing transit times in in vitro bioreactors. Microorganisms. 2019;7:641.
Article
PubMed Central
CAS
Google Scholar
Haange S-B, Jehmlich N, Krügel U, Hintschich C, Wehrmann D, Hankir M, Seyfried F, Froment J, Hübschmann T, Müller S, et al. Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. Microbiome. 2020;8:13.
Article
PubMed
PubMed Central
Google Scholar
Issa Isaac N, Philippe D, Nicholas A, Raoult D, Eric C. Metaproteomics of the human gut microbiota: challenges and contributions to other OMICS. Clin Mass Spectrom. 2019;14:18–30.
Article
PubMed
Google Scholar
Levi Mortera S, Soggiu A, Vernocchi P, Del Chierico F, Piras C, Carsetti R, Marzano V, Britti D, Urbani A, Roncada P, Putignani L. Metaproteomic investigation to assess gut microbiota shaping in newborn mice: a combined taxonomic, functional and quantitative approach. J Proteome. 2019;203:103378.
Article
CAS
Google Scholar
Warren AS, Archuleta J, Feng W-C, Setubal JC. Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics. 2010;11:131.
Article
PubMed
PubMed Central
CAS
Google Scholar
Storz G, Wolf YI, Ramamurthi KS. Small proteins can no longer be ignored. Annu Rev Biochem. 2014;83:753–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dinger ME, Pang KC, Mercer TR, Mattick JS. Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol. 2008;4:e1000176.
Article
PubMed
PubMed Central
CAS
Google Scholar
Su M, Ling Y, Yu J, Wu J, Xiao J. Small proteins: untapped area of potential biological importance. Front Genet. 2013;4:286.
Article
PubMed
PubMed Central
CAS
Google Scholar
Melior H, Maaß S, Li S, Förstner KU, Azarderakhsh S, Varadarajan AR, Stötzel M, Elhossary M, Barth-Weber S, Ahrens CH, Becher D, Evguenieva-Hackenberg E. The leader peptide peTrpL forms antibiotic-containing ribonucleoprotein complexes for posttranscriptional regulation of multiresistance genes. mBio. 2020 11(3):e01027–20. https://doi.org/10.1128/mBio.01027-20.
Sberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS. Large-scale analyses of human microbiomes reveal thousands of small, novel genes. Cell. 2019;178:1245–1259.e1214.
Article
CAS
PubMed
PubMed Central
Google Scholar
Petruschke H, Anders J, Stadler PF, Jehmlich N, von Bergen M. Enrichment and identification of small proteins in a simplified human gut microbiome. J Proteome. 2020;213:103604.
Article
CAS
Google Scholar
Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods. 2014;11:1114–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, et al. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res. 2017;27:2083–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fernández N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, et al. An integrated systems approach unveils new aspects of microoxia-mediated regulation in Bradyrhizobium diazoefficiens. Front Microbiol. 2019;10:924.
Article
PubMed
PubMed Central
Google Scholar
Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B. A proteogenomic resource enabling integrated analysis of listeria genotype-proteotype-phenotype relationships. J Proteome Res. 2020;19:1647–62.
Article
CAS
PubMed
Google Scholar
Mayjonade B, Gouzy J, Donnadieu C, Pouilly N, Marande W, Callot C, Langlade N, Muños S. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Biotechniques. 2016;61:203–5.
Article
CAS
PubMed
Google Scholar
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37:540–6.
Article
CAS
PubMed
Google Scholar
Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. In: arXiv e-prints; 2013. p. arXiv:1303.3997.
Google Scholar
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. In: arXiv e-prints; 2012. p. arXiv:1207.3907.
Google Scholar
Sović I, Šikić M, Wilm A, Fenlon SN, Chen S, Nagarajan N. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat Commun. 2016;7:11307.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018;15:461–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.
Article
PubMed
CAS
Google Scholar
Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32:292–4.
CAS
PubMed
Google Scholar
Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA. plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics. 2016;32:3380–7.
CAS
PubMed
Google Scholar
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol. 2017;34:2115–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
Article
PubMed
PubMed Central
CAS
Google Scholar
Singhal P, Jayaram B, Dixit SB, Beveridge DL. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations. Biophys J. 2008;94:4173–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods. 2007;4:923.
Article
PubMed
CAS
Google Scholar
Kim S, Pevzner PA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat Commun. 2014;5:5277.
Article
CAS
PubMed
Google Scholar
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol. 2012;30:918–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Qeli E, Ahrens CH. PeptideClassifier for protein inference and targeted quantitative proteomics. Nat Biotechnol. 2010;28:647–50.
Article
CAS
PubMed
Google Scholar
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17:3.
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data. Cambridge: Babraham Bioinformatics, Babraham Institute; 2010.
Google Scholar
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
PubMed
Google Scholar
Kämpf C, Specht M, Scholz A, Puppel S-H, Doose G, Reiche K, Schor J. Hackermüller J: uap: reproducible and robust HTS data analysis. BMC Bioinformatics. 2019;20:1–9.
Article
CAS
Google Scholar
Gasteiger E. et al. (2005) Protein Identification and Analysis Tools on the ExPASy Server. In: Walker J.M. (eds) The Proteomics Protocols Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1385/1-59259-890-0:571.
Käll L, Krogh A, Sonnhammer EL. A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 2004;338:1027–36.
Article
PubMed
CAS
Google Scholar
Veltri D, Kamath U, Shehu A. Deep learning improves antimicrobial peptide recognition. Bioinformatics. 2018;34:2740–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Castro E, Sigrist CJ, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Res. 2006;34:W362–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10:845–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zimmermann J, Kaleta C, Waschina S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. bioRxiv. 2020. https://doi.org/10.1101/2020.03.20.000737.
Aden K, Rehman A, Waschina S, Pan WH, Walker A, Lucio M, Nunez AM, Bharti R, Zimmerman J, Bethge J, et al. Metabolic functions of gut microbes associate with efficacy of tumor necrosis factor antagonists in patients with inflammatory bowel diseases. Gastroenterology. 2019;157:1279–1292.e1211.
Article
CAS
PubMed
Google Scholar
Team RC. R: a language and environment for statistical computing. Vienna: R Found Stat Comput; 2017.
Google Scholar
Wickham H. ggplot2: elegant graphics for data analysis: Springer; 2016. https://doi.org/10.1007/978-3-319-24277-4.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Swaney DL, Wenger CD, Coon JJ. Value of using multiple proteases for large-scale mass spectrometry-based proteomics. J Proteome Res. 2010;9:1323–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giansanti P, Tsiatsiani L, Low TY, Heck AJR. Six alternative proteases for mass spectrometry–based proteomics beyond trypsin. Nat Protoc. 2016;11:993–1006.
Article
CAS
PubMed
Google Scholar
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2006;5:2339–47.
Article
CAS
PubMed
Google Scholar
Omasits U, Quebatte M, Stekhoven DJ, Fortes C, Roschitzki B, Robinson MD, Dehio C, Ahrens CH. Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome. Genome Res. 2013;23:1916–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmidt A, Kochanowski K, Vedelaar S, Ahrné E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold R, Heinemann M. The quantitative and condition-dependent Escherichia coli proteome. Nat Biotechnol. 2016;34:104–10.
Article
CAS
PubMed
Google Scholar
Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteome. 2013;86:27–42.
Article
CAS
Google Scholar
Yount NY, Yeaman MR. Multidimensional signatures in antimicrobial peptides. Proc Natl Acad Sci U S A. 2004;101:7363–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duval M, Cossart P. Small bacterial and phagic proteins: an updated view on a rapidly moving field. Curr Opin Microbiol. 2017;39:81–8.
Article
CAS
PubMed
Google Scholar
Cassidy L, Prasse D, Linke D, Schmitz RA, Tholey A. Combination of bottom-up 2D-LC-MS and semi-top-down GelFree-LC-MS enhances coverage of proteome and low molecular weight short open reading frame encoded peptides of the Archaeon Methanosarcina mazei. J Proteome Res. 2016;15:3773–83.
Article
CAS
PubMed
Google Scholar
Müller SA, Kohajda T, Findeiß S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem. 2010;398:2867–81.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet. 2014;15:205–13.
Article
CAS
PubMed
Google Scholar
VanOrsdel CE, Kelly JP, Burke BN, Lein CD, Oufiero CE, Sanchez JF, Wimmers LE, Hearn DJ, Abuikhdair FJ, Barnhart KR, et al. Identifying new small proteins in Escherichia coli. Proteomics. 2018;18:1700064.
Article
PubMed Central
CAS
Google Scholar
Weaver J, Mohammad F, Buskirk AR, Storz G. Identifying small proteins by ribosome profiling with stalled initiation complexes. mBio. 2019;10(2):e02819–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen J, Brunner A-D, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS. Pervasive functional translation of noncanonical human open reading frames. Science. 2020;367:1140–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lohmann P, Schäpe SS, Haange S-B, Oliphant K, Allen-Vercoe E, Jehmlich N, Von Bergen M. Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics. Expert Rev Proteomics. 2020;17:163–73.
Article
CAS
PubMed
Google Scholar
Gouveia D, Pible O, Culotta K, Jouffret V, Geffard O, Chaumot A, Degli-Esposti D, Armengaud J. Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host. NPJ Biofilms Microbiomes. 2020;6:23.
Article
PubMed
PubMed Central
Google Scholar
Varadarajan AR, Allan RN, Valentin JDP, Castañeda Ocampo OE, Somerville V, Pietsch F, Buhmann MT, West J, Skipp PJ, van der Mei HC, et al. An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1. NPJ Biofilms Microbiomes. 2020;6:46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Muth T, Kolmeder CA, Salojärvi J, Keskitalo S, Varjosalo M, Verdam FJ, Rensen SS, Reichl U, de Vos WM, Rapp E, Martens L. Navigating through metaproteomics data: a logbook of database searching. PROTEOMICS. 2015;15:3439–53.
Article
CAS
PubMed
Google Scholar
Blakeley P, Overton IM, Hubbard SJ. Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res. 2012;11:5221–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nesvizhskii AI. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteome. 2010;73:2092–123.
Article
CAS
Google Scholar
Moreno-Gámez S, Sorg RA, Domenech A, Kjos M, Weissing FJ, van Doorn GS, Veening J-W. Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence. Nat Commun. 2017;8:854.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hayes CS, Aoki SK, Low DA. Bacterial contact-dependent delivery systems. Annu Rev Genet. 2010;44:71–90.
Article
CAS
PubMed
Google Scholar
Kelly G, Prasannan S, Daniell S, Fleming K, Frankel G, Dougan G, Connerton I, Matthews S. Structure of the cell-adhesion fragment of intimin from enteropathogenic Escherichia coli. Nat Struct Biol. 1999;6:313–8.
Article
CAS
PubMed
Google Scholar
Hamburger ZA, Brown MS, Isberg RR, Bjorkman PJ. Crystal structure of invasin: a bacterial integrin-binding protein. Science. 1999;286:291.
Article
CAS
PubMed
Google Scholar
Luo Y, Frey EA, Pfuetzner RA, Creagh AL, Knoechel DG, Haynes CA, Finlay BB, Strynadka NCJ. Crystal structure of enteropathogenic Escherichia coli intimin–receptor complex. Nature. 2000;405:1073–7.
Article
CAS
PubMed
Google Scholar
Barlow P. Grasping the nettle: a bacterial invasin that targets immunoglobulin variable domains. J Biol Chem. 2018;293:8691–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Castonguay AC, Olson LJ, Dahms NM. Mannose 6-phosphate receptor homology (MRH) domain-containing lectins in the secretory pathway. Biochim Biophys Acta. 1810;2011:815–26.
Google Scholar
Begg KJ, Dewar SJ, Donachie WD. A new Escherichia coli cell division gene, ftsK. J Bacteriol. 1995;177:6211.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alekshun MN, Levy SB. The mar regulon: multiple resistance to antibiotics and other toxic chemicals. Trends Microbiol. 1999;7:410–3.
Article
CAS
PubMed
Google Scholar
Alekshun MN, Levy SB, Mealy TR, Seaton BA, Head JF. The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 Å resolution. Nat Struct Biol. 2001;8:710–4.
Article
CAS
PubMed
Google Scholar
Raina M, Storz G. SgrT, a small protein that packs a sweet punch. J Bacteriol. 2017;199:e00130–17.
Article
PubMed
PubMed Central
Google Scholar
Hassan M, Kjos M, Nes IF, Diep DB, Lotfipour F. Natural antimicrobial peptides from bacteria: characteristics and potential applications to fight against antibiotic resistance. J Appl Microbiol. 2012;113:723–36.
Article
CAS
PubMed
Google Scholar
Koo T, Lee J, Hwang S. Development of an interspecies interaction model: an experiment on Clostridium cadaveris and Clostridium sporogenes under anaerobic condition. J Environ Manag. 2019;237:247–54.
Article
CAS
Google Scholar
Clarke DJ, Morris JG. Butyricin 7423: a Bacteriocin produced by Clostridium butyricum NCIB7423. Microbiology. 1976;95:67–77.
CAS
Google Scholar
Rolfe RD, Helebian S, Finegold SM. Bacterial interference between Clostridium difficile and normal fecal flora. J Infect Dis. 1981;143:470–5.
Article
CAS
PubMed
Google Scholar
Nissen-Meyer J, Nes IF. Ribosomally synthesized antimicrobial peptides: their function, structure, biogenesis, and mechanism of action. Arch Microbiol. 1997;167:67–77.
Article
CAS
PubMed
Google Scholar
Karpiński TM, Szkaradkiewicz AK. Characteristic of bacteriocines and their application. Pol J Microbiol. 2013;62:223–35.
Article
PubMed
Google Scholar
Barman S, Ghosh R, Mandal NC. Production optimization of broad spectrum bacteriocin of three strains of Lactococcus lactis isolated from homemade buttermilk. Ann Agrar Sci. 2018;16:286–96.
Article
Google Scholar
Ladha G, Jeevaratnam K. Characterization of purified antimicrobial peptide produced by Pediococcus pentosaceus LJR1, and its application in preservation of white leg shrimp. World J Microbiol Biotechnol. 2020;36:72.
Article
CAS
PubMed
Google Scholar