Siriraj Long-read Lab (Si-LoL) has launched a new product, BacBook, to support manufacturers of probiotic products and feed additives in assessing the suitability of bacterial strains and complying with European Food Safety Authority (EFSA) guidelines1,2. Our book includes a collection of whole genome sequencing WGS and bioinformatics analyzed results that provide valuable information about the characteristics of bacterial strains, including

• a search for antimicrobial peptides and bacteriocin

• a search of known antimicrobial resistant (AMR) genes

• gene annotation and plasmid prediction

• Phage identification

Why us?

•>6 years of experience on bacterial WGS with over 30 publications related to DNA sequencing technologies and bioinformatics.

•Apply state-of-the-art technology so-called Oxford Nanopore Technologies which has superior performance compared to current short-read technologies or 16S rRNA gene sequencing. The nanopore technology provides higher accuracy and resolution in bacterial species classification.

•We follow EFSA guideline by selecting a library preparation method that can capture small plasmids and apply EFSA-based sequencing strategy and quality control.

•BacBook (including raw and analyzed data) will be delivered via high-security Amazon Web Services cloud.

References:

1. Guidance on the characterization of microorganisms used as feed additives or as production organisms. doi: 10.2903/j.efsa.2018.5206, 2018

2. EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain. doi: 10.2903/j.efsa.2021.6506, 2021

*Si-LoL does not provide Phenotypic testing based on determination of a minimum inhibitory concentration (MIC).

BacBook Air - WGS + gene annotation

BacBook Pro - WGS + gene annotation + EFSA

Metabook - Nanopore-only metagenomics

Microbook - Full-length 16S sequencing (species level identification)

High resolution nanopore-based HLA-typing (11 loci)

Our Nanopore-related publications

·     Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing. Front. Genet., 23 June (2023) Sec. Pharmacogenetics and Pharmacogenomics. Volume 14 - 2023 | https://doi.org/10.3389/fgene.2023.1213457

·      Worarat Kruasuwan, Piroon Jenjaroenpun, Tantip Arigul, Nipa Chokesajjawatee, Pimlapas Leekitcharoenphon, Suporn Foongladda, Thidathip Wongsurawat. Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements. Scientific Reports volume 13, Article number: 4540 (2023)

·      Piya Chaemsaithong, Roberto Romero, Pisut Pongchaikul, Pornpun Vivithanaporn, Waranyu Lertrut, Adithep Jaovisidha, Paninee Mongkolsuk, Perapon Nitayanon, Khontawan Pongsuktavorn, Threebhorn Kamlungkuea, Eunjung Jung, Manaphat Suksai, Arunee Singhsnaeh, Piroon Jenjaroenpun, Iyarit Thaipisuttikul, Thidathip Wongsurawat. Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing. Journal of Perinatal Medicine. 13 Dec 2022, aop

·      Aunthikarn Sudjai, Kantgamon Suriye, Worarat Kruasuwan, Piroon Jenjaroenpun, Suporn Foongladda, Thidathip Wongsurawat. Long-Read 16S rRNA Amplicon and Metagenomic Data of Swine Feed-Additive Probiotics Product. Microbiology Resource Announcements. 2022/8/22, e00397-22

·      Thidathip Wongsurawat, Piroon Jenjaroenpun, Intawat Nookaew. Direct Sequencing of RNA and RNA Modification Identification Using Nanopore. Methods in molecular biology (Clifton, N.J.) May 2022, 2477:71-77

·      Thidathip Wongsurawat, Piroon Jenjaroenpun, Visanu Wanchai, Intawat Nookaew. Front. Bioeng. Biotechnol. Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae. Frontiers in Microbiology. Volume 10, Article 842299, 12 April 2022

·      Pimpayao Sodsai, Piroon Jenjaroenpun, Nattiya Hirankarn, Thidathip Wongsurawat, Suwatchareeporn Rotcheewaphan. Complete Genome Sequences of Mycobacterium farcinogenes Strains Isolated from Clinical Specimens from Patients in Thailand. Microbiol Resour Announc. 2021 Volume 10, Issue 46 e01005-21

·      Thidathip Wongsurawat, Nuntaya Punyadee, Piroon Jenjaroenpun, Dumrong Mairiang, Nattaya Tangthawornchaikul, Prida Malasit, Panisadee Avirutnan, Prapat Suriyaphol, Kwanrutai Chin-Inmanu. RNA Sequencing Data Sets and Their Whole-Genome Sequence Assembly of Dengue Virus from Three Serial Passages in Vero Cells. Microbiol Resource Announcements. Microbiol Resour Announc. 2021 Apr; 10(17): e00145-21.

·      Piroon Jenjaroenpun, Visanu Wanchai, Kikumi D. Ono-Moore, Jennifer Laudadio, Laura P. James, Sean H. Adams, Fred Prior, Intawat Nookaew, David W. Ussery, Thidathip Wongsurawat. Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing. Microbiol Resource Announcements. 17 Dec 2020. 10:e01109-20.

·      Thidathip Wongsurawat, Piroon Jenjaroenpun, Annick De Loose, Duah Alkam, David W Ussery, Intawat Nookaew, Yuet-Kin Leung, Shuk-Mei Ho, John D Day, Analiz Rodriguez. A novel Cas9-targeted long-read assay for simultaneous detection of IDH1/2 mutations and clinically relevant MGMT methylation in fresh biopsies of diffuse glioma. Acta Neuropathologica Communications. 20 June 2020. 8, Article number: 87

·      Sangam Kandel, Supaphen Sripiboon, Piroon Jenjaroenpun, David W Ussery, Intawat Nookaew, Michael S Robeson, Thidathip Wongsurawat. 16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in Thailand. Microbiology Resource Announcements. 20 June 2020. Volume 9 Issue 24

·      Thidathip Wongsurawat, Arundhati Gupta, Piroon Jenjaroenpun, Shana Owens, J Craig Forrest, Intawat Nookaew. R-loop-forming Sequences Analysis in Thousands of Viral Genomes Identify A New Common Element in Herpesviruses. Scientific Reports. 14 April 2020. Volume 10 Issue 1 Page 1-9

·      Piroon Jenjaroenpun†, Thidathip Wongsurawat†, Zulema Udaondo, Courtney Anderson, James Lopez, Meera Mohan, Ruslana Tytarenko, Brian Walker, Intawat Nookaew, David W. Ussery, Atul Kothari, Se-Ran Jun. Complete genome sequences of four isolates of vancomycin-resistant Enterococcus faecium with the vanA gene and two Daptomycin resistant mutations from two inpatients with Prolonged Bacteremia. Microbiology Resource Announcements. 6 February 2020. Volume 9 Issue 6 e01380-19

·      Thidathip Wongsurawat, Mayumi Nakagawa, Omar Atiq, Hannah N Coleman, Piroon Jenjaroenpun, James I Allred, Angela Trammel, Pantakan Puengrang, David W Ussery, Intawat Nookaew. An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients. Journal of Microbiological Methods. 1 November 2019. Volume 166. Page 105739 

·      Zulema Udaondo†, Thidathip Wongsurawat†, Piroon Jenjaroenpun, Courtney Anderson, James Lopez, Meera Mohan, Ruslana Tytarenko, Brian Walker, Intawat Nookaew, David Ussery, Atul Kothari, Se-Ran Jun. Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection. Microbiology Resource Announcements. 11 April 2019, Volume 8 Issue 15 e00222-19

·      Thidathip Wongsurawat†, Piroon Jenjaroenpun†, Mariah K Taylor, Jasper Lee, Aline Lavado Tolardo, Jothi Parvathareddy, Sangam Kandel, Taylor D Wadley, Bualan Kaewnapan, Niracha Athipanyasilp, Andrew M Skidmore, Donghoon Chung, Chutikarn Chaimayo, Michael Whitt, Wannee Kantakamalakul, Ruengpung Sutthent, Navin Horthongkham, David W Ussery, Colleen B Jonsson, Intawat Nookaew, Rapid Sequencing of Multiple RNA Viruses in their Native Form. Frontier in Microbiology, 25 February 2019. Volume 10 Article 260

·      Thidathip Wongsurawat†, Piroon Jenjaroenpun†, Niracha Athipanyasilp, Bualan Kaewnapan, Nattawat Leelahakorn, Nasikarn Angkasekwinai, Wannee Kantakamalakul, Ruengpung Sutthent, David W Ussery, Navin Horthongkham, Intawat Nookaew. Genome Sequences of Zika Virus Strains Recovered from Amniotic Fluid, Placenta, and Fetal Brain of a Microcephaly Patient in Thailand. Microbiology Resource Announcements, 20 September 2018. 7(11):e01020-18

·      Thidathip Wongsurawat†, Niracha Athipanyasilp†, Piroon Jenjaroenpun, Se-Ran Jun, Bualan Kaewnapan, Trudy M. Wassenaar, Nuttawut Leelahakorn, Nasikarn Angkasekwinai, Wannee Kantakamalakul, David W. Ussery, Ruengpung Sutthent, Intawat Nookaew, Navin Horthongkham, A Case of Microcephaly in Thailand Following Zika Virus Infection During Pregnancy. Emerging Infectious Diseases, September 2018. 24(9):1758

·      Piroon Jenjaroenpun†, Thidathip Wongsurawat†, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew. Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. †co-first author, Nucleic Acids Research, 20 April 2018, Volume 46, Issue 7, Pages e38

·      Jaime Brizuela, Rattagan Kajeekul, Thomas J Roodsant, Athita Riwload, Parichart Boueroy, Auttapong Pattanapongpaibool, Janjira Thaipadungpanit, Piroon Jenjaroenpun, Thidathip Wongsurawat, Elizabeth M Batty, Boas CL van der Putten, Constance Schultsz, Anusak Kerdsin. Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand. Microbial Genomics. Microbiology Society. Volume 9 Issue 2 page 000952

·      Kwanjeera Wanichthanarak, Intawat Nookaew, Phongthana Pasookhush, Thidathip Wongsurawat, Piroon Jenjaroenpun, Namkhang Leeratsuwan, Songsak Wattanachaisaereekul, Wonnop Visessanguan, Yongyut Sirivatanauksorn, Narong Nuntasaen, Chutima Kuhakarn, Vichai Reutrakul, Pravech Ajawatanawong, Sakda Khoomrung. Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae. BMC Plant Biology. 2023/12, 1-22

·      Complete Genome Sequences of Three Salmonella Strains Obtained from a Poultry Production Farm in Thailand. Tantip Arigul, Piroon Jenjaroenpun, Natnicha Wankaew, Juthatip Vespirom, Phatcharaporn Thuamkaew, Thidathip Wongsurawat, Sudarat Ledlod. Microbiology Resource Announcements. 2023/1/18. e01104-22.

·      Parichart Boueroy, Thidathip Wongsurawat, Piroon Jenjaroenpun, Peechanika Chopjitt, Rujirat Hatrongjit, Sathaporn Jittapalapong, Anusak Kerdsin. Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand. Scientific Reports, Volume 12, Issue 1, Pages 1-12

·      Natakorn Nokchan, Thidathip Wongsurawat, Piroon Jenjaroenpun, Perapon Nitayanon, Chanwit Tribuddharat. Whole-genome sequence analysis of high-level penicillin-resistant strains and antimicrobial susceptibility of Neisseria gonorrhoeae clinical isolates from Thailand. Plos One, July 29, 2022. https://doi.org/10.1371/journal.pone.0271657

·      Zulema Udaondo, Kaleb Z. Abram, Trent Gulley, Kelley Garner, Jennifer Shray, Mary Whisnant, Ashley Harris-Spotts, Maui Crawford, Atul Kothari, Thidathip Wongsurawat, Sun-Hee Moon, En Huang, Se-Ran Jun. Complete Genome Sequence of a Non-Carbapenemase-Producing Carbapenem-Resistant Providencia rettgeri Strain Isolated from a Clinical Urine Sample in Arkansas. Microbiol Resour Announc. 2022

·      Nathita Phumthanakorn, Thidathip Wongsurawat, Piroon Jenjaroenpun, Alongkorn Kurilung, Nuvee Prapasarakul. Novel Organization of the Staphylococcal Cassette Chromosome mec Composite Island in Clinical Staphylococcus haemolyticus and Staphylococcus hominis Subspecies hominis Isolates from Dogs. 5 July 2022, https://doi.org/10.1128/spectrum.00997-22.

·      Rasmus Amund Henriksen, Piroon Jenjaroenpun, Ida Borup Sjøstrøm, Kristian Reveles Jensen, Iñigo Prada-Luengo, Thidathip Wongsurawat, Intawat Nookaew, Birgitte Regenberg. Circular DNA in the human germline and its association with recombination. 2021. Molecular Cell 82, 1–9.

·      Naris Kueakulpattana, Dhammika Leshan Wannigama, Sirirat Luk-in, Parichart Hongsing, Cameron Hurst, Vishnu Nayak Badavath, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nipat Teeratakulpisan, Stephen J. Kerr, Shuichi Abe, Phatthranit Phattharapornjaroen, Aye Mya Sithu Shein, Thammakorn Saethang, Naphat Chantaravisoot, Mohan Amarasiri, Paul G. Higgins & Tanittha Chatsuwan. Multidrug-resistant Neisseria gonorrhoeae infection in heterosexual men with reduced susceptibility to ceftriaxone, first report in Thailand. Scientific Reports volume 11, Article number: 21659 (2021)

·      Thitima Cherdtrakulkiat, Thidathip Wongsurawat, Piroon Jenjaroenpun, Sawannee Sutheeworapong, Wanna Leelawiwat, Joseph V. Woodring, Eileen F. Dunne, John R. Papp, Somporn Srifuengfung, Chanwit Tribuddharati. Complete Genome Sequence of Neisseria gonorrhoeae Multilocus Sequence Type ST7363 Isolated from Thailand. Microbiol Resour Announc. 2021 Volume 10 Issue 41 e00573-21

·      Duah Alkam, Thidathip Wongsurawat, Intawat Nookaew, Anthony R Richardson, David Ussery, Mark S Smeltzer, Piroon Jenjaroenpun. Microbial Genomics. Is amplification bias consequential in transposon sequencing (TnSeq) assays? A case study with a Staphylococcus aureus TnSeq library subjected to PCR-based and amplification-free enrichment methods, 01 October 2021, Volume 7, Issue 10, page 000655

·      Zulema Udaondo, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri, Intawat Nookaew. Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon. Life 2021, 11(8), 862

·      Peechanika Chopjitt, Thidathip Wongsurawat, Piroon Jenjaroenpun, Parichart Boueroy, Watcharaporn Kamjumphol, Rujirat Hatrongjit, Anusak Kerdsin. Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Harboring Staphylococcal Cassette Chromosome mec Type IX, Isolated from a Fatal Bacteremic Pneumonia Case. Microbiol Resour Announc. 2021 July; 10(30): e00616-21.

·      Pattapon Kunadirek, Natthaya Chuaypen, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nutcha Pinjaroen, Pongserath Sirichindakul, Intawat Nookaew, Pisit Tangkijvanich. Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand. Cancers 2021, 13(9), 2229.

·      Tanaporn Uengwetwanit, Wirulda Pootakham, Intawat Nookaew, Chutima Sonthirod, Pacharaporn Angthong, Kanchana Sittikankaew, Wanilada Rungrassamee, Sopacha Arayamethakorn, Thidathip Wongsurawat, Piroon Jenjaroenpun, Duangjai Sangsrakru, Rungnapa Leelatanawit, Jutatip Khudet , Jasper J. Koehorst,  Peter J. Schaap,  Vitor Martins dos Santos.  Frédéric Tangy,  Nitsara Karoonuthaisiri. A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes. Mol Ecol Resour. 2021 Feb 15

·      Suganya Yongkiettrakul, Thidathip Wongsurawat, Piroon Jenjaroenpun, Daniel A Acheampong, Potjanee Srimanote, Krissana Maneerat, Wonnop Visessanguan, Intawat Nookaew. Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand. Infection, Genetics and Evolution. 13 Dec 2020. 11;104674.

·      Rujirat Hatrongjit, Anusak Kerdsin, Dan Takeuchi, Thidathip Wongsurawat, Piroon Jenjaroenpun, Peechanika Chopjitt, Parichart Boueroy, Yukihiro Akeda, Shigeyuki Hamada. Genomic Analysis of Aeromonas veronii C198, a Novel Mcr-3.41-Harboring Isolate from a Patient with Septicemia in Thailand. Pathogens 2020, 9, 1031

·      Shivang Desai, Ahmad Baghal, Thidathip Wongsurawat, Piroon Jenjaroenpun, Thomas Powell, Shaymaa Al-Shukri, Kim Gates, Phillip Farmer, Michael Rutherford, Geri Blake, Tracy Nolan, Kevin Sexton, William Bennett, Kirk Smith, Shorabuddin Syed, Fred Prior. Chest imaging representing a COVID-19 positive rural U.S. population. Scientific Data. 24 November 2020. Volume 7, Article number: 414

·      Pattsarun Cheawchanlertfa, Sawannee Sutheeworapong, Piroon Jenjaroenpun, Thidathip Wongsurawat, Intawat Nookaew, Supapon Cheevadhanarak, Akihiko Kosugi, Patthra Pason, Rattiya Waeonukul, Khanok Ratanakhanokchai, Chakrit Tachaapaikoon. Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. 16 November 2020 PeerJ 8: e10343

·      Mariah K Taylor, Evan P Williams, Thidathip Wongsurawat, Piroon Jenjaroenpun, Intawat Nookaew, Colleen B Jonsson. Amplicon-based, next-generation sequencing approaches to characterize single nucleotide polymorphisms of Orthohantavirus species. Frontiers in Cellular and Infection Microbiology, October 2020, Volume 10, Article 565591

·      Peechanika Chopjitt, Thidathip Wongsurawat, Piroon Jenjaroenpun, Parichart Boueroy, Rujirat Hatrongjit, Anusak Kerdsin. Complete Genome Sequences of Four Extensively Drug-Resistant Acinetobacter baumannii Isolates from Thailand. Microbiology Resource Announcements. 1 October 2020. Volume 9 Issue 40, e00949-20

·      Natapol Pornputtapong, Daniel A Acheampong, Preecha Patumcharoenpol, Piroon Jenjaroenpun, Thidathip Wongsurawat, Se-Ran Jun, Suganya Yongkiettrakul, Nipa Chokesajjawatee, Intawat Nookaew. KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. Frontiers in Bioengineering and Biotechnology. 23 September 2020. Volume 8 Page 1080

·      Piroon Jenjaroenpun, Thidathip Wongsurawat, Taylor D Wadley, Trudy M Wassenaar, Jun Liu, Qing Dai, Visanu Wanchai, Nisreen S Akel, Azemat Jamshidi-Parsian, Aime T Franco, Gunnar Boysen, Michael L Jennings, David W Ussery, Chuan He, Intawat Nookaew. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Research. gkaa620, 25 July 2020

·      Intawat Nookaew, Piroon Jenjaroenpun, Hua Du, Pengcheng Wang, Jun Wu, Thidathip Wongsurawat, Sun Hee Moon, En Huang, Yinsheng Wang, Gunnar Boysen. Detection and discrimination of DNA adducts differing in size, regiochemistry and functional group by nanopore sequencing. 17 August 2020. Chemical Research in Toxicology

·      Nipa Chokesajjawatee, Pannita Santiyanont, Kanittha Chantarasakha, Kanokarn Kocharin, Chinae Thammarongtham, Supatcha Lertampaiporn, Tayvich Vorapreeda, Tanawut Srisuk, Thidathip Wongsurawat, Piroon Jenjaroenpun, Intawat Nookaew, Wonnop Visessanguan. Safety Assessment of a Nham Starter Culture Lactobacillus plantarum BCC9546 via Whole-genome Analysis. Scientific Reports. 24 June 2020. Volume 10, Issue 1, 1-20

·      Zulema Udaondo, Piroon Jenjaroenpun, Thidathip Wongsurawat, Erik Meyers, Courtney Anderson, James Lopez, Meera Mohan, Ruslana Tytarenko, Brian Walker, David Ussery, Atul Kothari, Se-Ran Jun. Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing. Open Forum Infectious Diseases. 23 May 2020. Volume 7, Issue 6, ofaa180