Angelescu I R, Zamfir M, Stancu M M, Grosu-Tudor S S. 2019. Identification and probiotic properties of lactobacilli isolated from two different fermented beverages. Annals of Microbiology, 69, 1557–1565.

Antipov D, Korobeynikov A, Mclean J S, Pevzner P A. 2016. hybridSPAdes: An algorithm for hybrid assembly of short and long reads. Bioinformatics, 32, 1009–1015.

Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende D R, Fernandes G R, Tap J, Bruls T, Batto J M, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, et al. 2011. Enterotypes of the human gut microbiome. Nature, 473, 174–180.

Bankevich A, Nurk S, Antipov D, Gurevich A A, Dvorkin M, Kulikov A S, Lesin V M, Nikolenko S I, Pham S, Prjibelski A D, Pyshkin A V, Sirotkin A V, Vyahhi N, Tesler G, Alekseyev M A, Pevzner P A. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19, 455–477.

Beck L C, Masi A C, Young G R, Vatanen T, Lamb C A, Smith R, Coxhead J, Butler A, Marsland B J, Embleton N D. 2022. Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants. Nature Microbiology, 7, 1525–1535.

Bermudez-Brito M, Plaza-Diaz J, Munoz-Quezada S, Gomez-Llorente C, Gil A. 2012. Probiotic mechanisms of action. Annals of Nutrition and Metabolism, 61, 160–174.

Bertrand D, Shaw J, Kalathiyappan M, Ng A H Q, Kumar M S, Li C, Dvornicic M, Soldo J P, Koh J Y, Tong C, Ng O T, Barkham T, Young B, Marimuthu K, Chng K R, Sikic M, Nagarajan N. 2019. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nature Biotechnology, 37, 937–944.

Bickhart D M, Kolmogorov M, Tseng E, Portik D M, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan S T, Shin S B, Zorea A, Andreu V P, Panke-Buisse K, Medema M H, Mizrahi I, Pevzner P A, Smith T P L. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology, 40, 711–719.

Birol I, Jackman S D, Nielsen C B, Qian J Q, Varhol R, Stazyk G, Morin R D, Zhao Y, Hirst M, Schein J E. 2009. De novo transcriptome assembly with ABySS. Bioinformatics (Oxford, England), 25, 2872–2877.

Burton J N, Adey A, Patwardhan R P, Qiu R, Kitzman J O, Shendure J. 2013. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology, 31, 1119–1125.

Camille T, Paula Z A, Vivian G, Patrícia B, Kenia D C, Eliane D. 2021. Does probiotic consumption enhance wound healing? A systematic review. Nutrients, 14, 111.

Canfora E E, Jocken J W, Blaak E E. 2015. Short-chain fatty acids in control of body weight and insulin sensitivity. Nature Reviews Endocrinology, 11, 577–591.

Chin C S, Alexander D H, Marks P, Klammer A A, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler E E, Turner S W, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10, 563–569.

Costa V, Angelini C, De Feis I, Ciccodicola A. 2010. Uncovering the complexity of transcriptomes with RNA-Seq. Journal of Biomedicine and Biotechnology, 2010, 853916.

Devlin A S, Fischbach M A. 2015. A biosynthetic pathway for a prominent class of microbiota-derived bile acids. Nature Chemical Biology, 11, 685–690.

Dinghua L, Chi-Man L, Ruibang L, Kunihiko S, Tak-Wah L. 2015. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics (Oxford, England), 31, 1674–1676.

Dudchenko O, Batra S S, Omer A D, Nyquist S K, Hoeger M, Durand N C, Shamim M S, Machol I, Lander E S, Aiden A P, Aiden E L. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 356, 92–95.

El-Baky R M A, Farhan S M, Ibrahim R A, Mahran K M, Hetta H F. 2020. Antimicrobial resistance pattern and molecular epidemiology of ESBL and MBL producing Acinetobacter baumannii isolated from hospitals in Minia, Egypt. Alexandria Journal of Medicine, 56, 4–13.

El-Ghazely M H, Mahmoud W H, Atia M A, Eldip E M. 2016. Effect of probiotic administration in the therapy of pediatric thermal burn. Annals of Burns and Fire Disasters, 29, 268–272.

Eloe-Fadrosh E A, Brady A, Crabtree J, Drabek E F, Ma B, Mahurkar A, Ravel J, Haverkamp M, Fiorino A M, Botelho C, Andreyeva I, Hibberd P L, Fraser C M. 2015. Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio, 6, e00231–15.

Esposito C, Roberti A, Turra F, Cerulo M, Severino G, Settimi A, Escolino M. 2018. Frequency of antibiotic-associated diarrhea and related complications in pediatric patients who underwent hypospadias repair: A comparative study using probiotics vs placebo. Probiotics and Antimicrobial Proteins, 10, 323–328.

Evivie S E, Abdelazez A, Li B, Bian X, Li W, Du J, Huo G, Liu F. 2019. In vitro organic acid production and in vivo food pathogen suppression by probiotic S. thermophilus and L. bulgaricus. Frontiers in Microbiology, 10, 782.

Feng J, Wang L, Zhou L, Yang X, Zhao X. 2016. Using in vitro immunomodulatory properties of lactic acid bacteria for selection of probiotics against Salmonella infection in broiler chicks. PLoS ONE, 11, e0147630.

Feng P Y, Yang J F, Zhao S, Ling Z M, Han R, Wu Y, Ei-Sayed S, Kakade A, Khan A, Jin W L, Zhang W B, Byong Hun J, Fan J J, Liu M R, Mamtimin T, Liu P, Li X K. 2022. Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome. Npj Biofilms and Microbiomes, 8, 63.

Feng X, Cheng H, Portik D, Li H. 2022. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods, 19, 671–674.

Fijan S. 2014. Microorganisms with claimed probiotic properties: An overview of recent literature. International Journal of Environmental Research and Public Health, 11, 4745–4767.

Frese S A, Parker K, Calvert C C, Mills D A. 2015. Diet shapes the gut microbiome of pigs during nursing and weaning. Microbiome, 3, 1–10.

Fulde M, Hornef M W. 2014. Maturation of the enteric mucosal innate immune system during the postnatal period. Immunological Reviews, 260, 21–34.

Gao G, Ma T, Zhang T, Jin H, Li Y, Kwok L Y, Zhang H, Sun Z. 2021. Adjunctive probiotic Lactobacillus rhamnosus probio-M9 administration enhances the effect of anti-PD-1 antitumor therapy via restoring antibiotic-disrupted gut microbiota. Frontiers in Immunology, 12, 772532.

Ghurye J, Rhie A, Walenz B P, Schmitt A, Selvaraj S, Pop M, Phillippy A M, Koren S. 2019. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. PLoS Computational Biology, 15, e1007273.

Haiser H J, Gootenberg D B, Chatman K, Sirasani G, Balskus E P, Turnbaugh P J. 2013. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science, 341, 295–298.

Ijssennagger N, Belzer C, Hooiveld G J, Dekker J, Van Mil S W, Müller M, Kleerebezem M, Van Der Meer R. 2015. Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon. Proceedings of the National Academy of Sciences of the United States of America, 112, 10038–10043.

Janda J M, Abbott S L. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. Journal of Clinical Microbiology, 45, 2761–2764.

Jin H, Quan K, He Q, Kwok L Y, Ma T, Li Y, Zhao F, You L, Zhang H, Sun Z. 2023. A high-quality genome compendium of the human gut microbiome of Inner Mongolians. Nature Microbiology, 8, 150–161.

Johnson C H, Ivanisevic J, Siuzdak G. 2016. Metabolomics: Beyond biomarkers and towards mechanisms. Nature Reviews Molecular Cell Biology, 17, 451–459.

Juhi A, Gaurav S, Mayur K. 2013. Probiotics and their effects on metabolic diseases: An update. Journal of Clinical and Diagnostic Research, 7, 173–177.

Kamada N, Chen G Y, Inohara N, Núñez G. 2013. Control of pathogens and pathobionts by the gut microbiota. Nature Immunology, 14, 685–690.

Kim C Y, Ma J, Lee I. 2022. HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. Nature Communications, 13, 6367.

Kolmogorov M, Bickhart D M, Behsaz B, Gurevich A, Rayko M, Shin S B, Kuhn K, Yuan J, Polevikov E, Smith T P L, Pevzner P A. 2020. metaFlye: Scalable long-read metagenome assembly using repeat graphs. Nature Methods, 17, 1103–1110.

Kondo S, Xiao J Z, Satoh T, Odamaki T, Takahashi S, Sugahara H, Yaeshima T, Iwatsuki K, Kamei A, Abe K. 2010. Antiobesity effects of Bifidobacterium breve strain B-3 supplementation in a mouse model with high-fat diet-induced obesity. Bioscience, Biotechnology, and Biochemistry, 74, 1656–1661.

Kong S, Li Q, Zhang G, Li Q, Huang Q, Huang L, Zhang H, Huang Y, Peng Y, Qin B, Zhang Y. 2020. Exonuclease combinations reduce noises in 3D genomics technologies. Nucleic Acids Research, 48, e44.

Kong S, Zhang Y. 2019. Deciphering Hi-C: From 3D genome to function. Cell Biology and Toxicology, 35, 15–32.

Kruasuwan W, Jenjaroenpun P, Arigul T, Chokesajjawatee N, Leekitcharoenphon P, Foongladda S, Wongsurawat T. 2023. Nanopore sequencing discloses compositional quality of commercial probiotic feed supplements. Scientific Reports, 13, 4540.

Lamari F, Mahdhi A, Chakroun I, Esteban M A, Mazurais D, Amina B, Gatesoupe F J. 2016. Interactions between candidate probiotics and the immune and antioxidative responses of European sea bass (Dicentrarchus labrax) larvae. Journal of Fish Diseases, 39, 1421–1432.

Lau L Y J, Chye F Y. 2018. Antagonistic effects of Lactobacillus plantarum 0612 on the adhesion of selected foodborne enteropathogens in various colonic environments. Food Control, 91, 237–247.

Li J, Sung C Y, Lee N, Ni Y, Pihlajamaki J, Panagiotou G, El-Nezami H. 2016. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proceedings of the National Academy of Sciences of the United States of America, 113, E1306–E1315.

Liévin-Le Moal V. 2016. A gastrointestinal anti-infectious biotherapeutic agent: The heat-treated Lactobacillus LB. Therapeutic Advances in Gastroenterology, 9, 57–75.

Liu H, Zhang J, Zhang S, Yang F, Thacker P A, Zhang G, Qiao S, Ma X. 2014. Oral administration of Lactobacillus fermentum I5007 favors intestinal development and alters the intestinal microbiota in formula-fed piglets. Journal of Agricultural and Food Chemistry, 62, 860–866.

Lukic J, Chen V, Strahinic I, Begovic J, Lev-Tov H, Davis S C, Tomic-Canic M, Pastar I. 2017. Probiotics or pro-healers: The role of beneficial bacteria in tissue repair. Wound Repair and Regeneration, 25, 912–922.

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung D W, et al. 2012. SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.

Lynch S V, Pedersen O. 2016. The human intestinal microbiome in health and disease. The New England Journal of Medicine, 375, 2369–2379.

Mackowiak P A. 2013. Recycling Metchnikoff: Probiotics, the intestinal microbiome and the quest for long life. Frontiers in Public Health, 1, 52.

Manor O, Dai C L, Kornilov S A, Smith B, Price N D, Lovejoy J C, Gibbons S M, Magis A T. 2020. Health and disease markers correlate with gut microbiome composition across thousands of people. Nature Communications, 11, 5206.

Marchesi J R, Adams D H, Fava F, Hermes G D, Hirschfield G M, Hold G, Quraishi M N, Kinross J, Smidt H, Tuohy K M, Thomas L V, Zoetendal E G, Hart A. 2016. The gut microbiota and host health: A new clinical frontier. Gut, 65, 330–339.

Martinez F A C, Domínguez J M, Converti A, De Souza Oliveira R P. 2015. Production of bacteriocin-like inhibitory substance by Bifidobacterium lactis in skim milk supplemented with additives. Journal of Dairy Research, 82, 350–355.

Mcnulty N P, Yatsunenko T, Hsiao A, Faith J J, Muegge B D, Goodman A L, Henrissat B, Oozeer R, Cools-Portier S, Gobert G. 2011. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Science Translational Medicine, 3, 106ra106.

Michael T P, Jupe F, Bemm F, Motley S T, Sandoval J P, Lanz C, Loudet O, Weigel D, Ecker J R. 2018. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nature Communications, 9, 541.

Mohseni S, Bayani M, Bahmani F, Tajabadi-Ebrahimi M, Bayani M A, Jafari P, Asemi Z. 2018. The beneficial effects of probiotic administration on wound healing and metabolic status in patients with diabetic foot ulcer: A randomized, double-blind, placebo-controlled trial. Diabetes/Metabolism Research and Reviews, 34, e2970.

Moritz D, Howe B, Heer J. 2019. Falcon: Balancing interactive latency and resolution sensitivity for scalable linked visualizations. In: Proceedings of the 2019 CHI Conference on Human Factors in Computing Systems. 02 May, 2019, Glasgow, Scotland UK. https://doi.org/10.1145/3290605.3300924

Moss E L, Maghini D G, Bhatt A S. 2020. Complete, closed bacterial genomes from microbiomes using nanopore sequencing. Nature Biotechnology, 38, 701–707.

Neuman H, Debelius J W, Knight R, Koren O. 2015. Microbial endocrinology: The interplay between the microbiota and the endocrine system. FEMS Microbiology Reviews, 39, 509–521.

Nurk S, Meleshko D, Korobeynikov A, Pevzner P A. 2017. metaSPAdes: A new versatile metagenomic assembler. Genome Research, 27, 824–834.

Nurk S, Walenz B P, Rhie A, Vollger M R, Logsdon G A, Grothe R, Miga K H, Eichler E E, Phillippy A M, Koren S. 2020. HiCanu: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Research, 30, 1291–1305.

Oliva S, Nardo G D, Ferrari F, Mallardo S, Rossi P, Patrizi G, Cucchiara S, Stronati L. 2012. Randomised clinical trial: The effectiveness of Lactobacillus reuteri ATCC 55730 rectal enema in children with active distal ulcerative colitis. Alimentary Pharmacology & Therapeutics, 35, 327–334.

Panigrahi P, Parida S, Nanda N C, Satpathy R, Pradhan L, Chandel D S, Baccaglini L, Mohapatra A, Mohapatra S S, Misra P R, Chaudhry R, Chen H H, Johnson J A, Glenn Morris J, Paneth N, Gewolb I H. 2017. A randomized synbiotic trial to prevent sepsis among infants in rural India. Nature, 548, 407–412.

Peng Y, Leung H C, Yiu S M, Chin F Y. 2012. IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28, 1420–1428.

Pennisi E. 2010. Body’s hardworking microbes get some overdue respect. Science, 330, 1619.

Putnam N H, O’connell B L, Stites J C, Rice B J, Blanchette M, Calef R, Troll C J, Fields A, Hartley P D, Sugnet C W, Haussler D, Rokhsar D S, Green R E. 2016. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Research, 26, 342–350.

Qiang H Z X. 2021. Advances in the histology study, function and application of insect intestinal flora. Biotechnology Bulletin, 37, 102–112.

Rahayu E S, Mariyatun M, Putri Manurung N E, Hasan P N, Therdtatha P, Mishima R, Komalasari H, Mahfuzah N A, Pamungkaningtyas F H, Yoga W K, Nurfiana D A, Liwan S Y, Juffrie M, Nugroho A E, Utami T. 2021. Effect of probiotic Lactobacillus plantarum Dad-13 powder consumption on the gut microbiota and intestinal health of overweight adults. World Journal of Gastroenterol, 27, 107–128.

Reinhardt C, Bergentall M, Greiner T U, Schaffner F, Östergren-Lundén G, Petersen L C, Ruf W, Bäckhed F. 2012. Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling. Nature, 483, 627–631.

Ren J, He F, Yu D, Xu H, Li N, Cao Z, Wen J. 2023. 16S rRNA gene amplicon sequencing of gut microbiota affected by four probiotic strains in mice. Veterinary Sciencs, 10, 288.

Sekirov I, Russell S L, Antunes L C M, Finlay B B. 2010. Gut microbiota in health and disease. Physiological Reviews, 90, 859–904.

Seo B, Rather I, Kumar V, Choi U, Moon M, Lim J, Park Y. 2012. Evaluation of Leuconostoc mesenteroides YML003 as a probiotic against low-pathogenic avian influenza (H9N2) virus in chickens. Journal of Applied Microbiology, 113, 163–171.

Servant N, Varoquaux N, Lajoie B R, Viara E, Chen C J, Vert J P, Heard E, Dekker J, Barillot E. 2015. HiC-Pro: An optimized and flexible pipeline for Hi-C data processing. Genome Biology, 16, 259.

Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen H E, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck F J, Marschall T, Mayes S, Costa V, Zook J M, Liu K J, Kilburn D, Sorensen M, Munson K M, Vollger M R, et al. 2020. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nature Biotechnology, 38, 1044–1053.

Shakibaie M, Mohammadi-Khorsand T, Adeli-Sardou M, Jafari M, Amirpour-Rostami S, Ameri A, Forootanfar H. 2017. Probiotic and antioxidant properties of selenium-enriched Lactobacillus brevis LSe isolated from an Iranian traditional dairy product. Journal of Trace Elements in Medicine and Biology, 40, 1–9.

Shin J, Noh J R, Choe D, Lee N, Song Y, Cho S, Kang E J, Go M J, Ha S K, Kim J H, Kim Y H, Kim K S, Kim B C, Lee C H, Cho B K. 2022. Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models. Scientific Data, 9, 197.

Strozzi G P, Mogna L. 2008. Quantification of folic acid in human feces after administration of Bifidobacterium probiotic strains. Journal of Clinical Gastroenterology, 42, S179–S184.

Sudha M R, Ahire J J, Jayanthi N, Tripathi A, Nanal S. 2019. Effect of multi-strain probiotic (UB0316) in weight management in overweight/obese adults: A 12-week double blind, randomised, placebo-controlled study. Beneficial Microbes, 10, 855–866.

Sun Y, Liu M, Tang X, Zhou Y, Zhang J, Yang B. 2023. Culture-delivery live probiotics dressing for accelerated infected wound healing. ACS Applied & Materials & Interfaces, 15, 53283–53296.

Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S. 2019. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome, 7, 119.

Tokarz J, Haid M, Cecil A, Prehn C, Artati A, Moller G, Adamski J. 2017. Endocrinology meets metabolomics: Achievements, pitfalls, and challenges. Trends in Endocrinology & Metabolism, 28, 705–721.

De Vos W M, Tilg H, Van Hul M, Cani P D. 2022. Gut microbiome and health: Mechanistic insights. Gut, 71, 1020–1032.

Wang J, Zhang J, Liu W, Zhang H, Sun Z. 2021. Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut. NPJ Biofilms and Microbiomes, 7, 55.

Wang J W, Kuo C H, Kuo F C, Wang Y K, Hsu W H, Yu F J, Hu H M, Hsu P I, Wang J Y, Wu D C. 2019. Fecal microbiota transplantation: Review and update. Journal of the Formosan Medical Association, 118 (Suppl 1), S23-S31.

Wang Y, Liu X, Jia H, Zhang R, Guan J, Zhang L. 2022. Integrative analysis of transcriptome and metabolome reveals probiotic effects on cecal metabolism in broilers. Journal of the Science of Food and Agriculture, 103, 2876–2888.

Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57.

Westfall S, Carracci F, Estill M, Zhao D, Wu Q L, Shen L, Simon J, Pasinetti G M. 2021. Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract. Scientific Reports, 11, 1067.

Wood D E, Salzberg S L. 2014. Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biology, 15, R46.

Wu H, Tremaroli V, Schmidt C, Lundqvist A, Olsson L M, Kramer M, Gummesson A, Perkins R, Bergstrom G, Backhed F. 2020. The gut microbiota in prediabetes and diabetes: A population-based cross-sectional study. Cell Metabolism, 32, 379–390. e373.

Xu X, Xu P, Ma C, Tang J, Zhang X. 2013. Gut microbiota, host health, and polysaccharides. Biotechnology Advances, 31, 318–337.

Yan F, Polk D B. 2011. Probiotics and immune health. Current Opinion in Gastroenterology, 27, 496–501.

Yang C, Chowdhury D, Zhang Z, Cheung W K, Lu A, Bian Z, Zhang L. 2021. A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Computational and Structural Biotechnology Journal, 19, 6301–6314.

Yano J M, Yu K, Donaldson G P, Shastri G G, Ann P, Ma L, Nagler C R, Ismagilov R F, Mazmanian S K, Hsiao E Y. 2015. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell, 161, 264–276.

Yeh A, Morowitz M J. 2018. Probiotics and fecal microbiota transplantation in surgical disorders. Seminars in Colon & Rectal Surgery, 29, 37–43.

Zhang Z, Yang C, Veldsman W P, Fang X, Zhang L. 2023. Benchmarking genome assembly methods on metagenomic sequencing data. Briefings in Bioinformatics, 24, bbad087.

Zhao W, Yuan T, Piva C, Spinard E J, Schuttert C W, Rowley D C, Nelson D R. 2019. The probiotic bacterium phaeobacter inhibens downregulates virulence factor transcription in the shellfish pathogen vibrio coralliilyticus by N-Acyl homoserine lactone production. Applied and Environmental Microbiology, 85, e01545–18.

Zhou R, Li S, Yao W, Xie C, Chen Z, Zeng Z, Wang D, Xu K, Shen Z, Mu Y, Bao W, Jiang W, Li R, Liang Q, Li K. 2021. The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication. Molecular Ecology Resources, 21, 2077–2092.