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Heng S, Sutheeworapong S, Wangnai C, Champreda V, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C, Ceballos RM. Hydrolysis of ionic liquid-treated substrate with an Iocasia fonsfrigidae strain SP3-1 endoglucanase. Appl Microbiol Biotechnol 2024; 108:63. [PMID: 38189956 PMCID: PMC10774164 DOI: 10.1007/s00253-023-12918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Recently, we reported the discovery of a novel endoglucanase of the glycoside hydrolase family 12 (GH12), designated IfCelS12A, from the haloalkaliphilic anaerobic bacterium Iocasia fonsfrigidae strain SP3-1, which was isolated from a hypersaline pond in the Samut Sakhon province of Thailand (ca. 2017). IfCelS12A exhibits high substrate specificity on carboxymethyl cellulose and amorphous cellulose but low substrate specificity on b-1,3;1,4-glucan. Unlike some endoglucanases of the GH12 family, IfCelS12A does not exhibit hydrolytic activity on crystalline cellulose (i.e., Avicel™). High-Pressure Liquid Chromatography (HPLC) and Thin Layer Chromatography (TLC) analyses of products resulting from IfCelS12-mediated hydrolysis indicate mode of action for this enzyme. Notably, IfCelS12A preferentially hydrolyzes cellotetraoses, cellopentaoses, and cellohexaoses with negligible activity on cellobiose or cellotriose. Kinetic analysis with cellopentaose and barely b-D-glucan as cellulosic substrates were conducted. On cellopentaose, IfCelS12A demonstrates a 16-fold increase in activity (KM = 0.27 mM; kcat = 0.36 s-1; kcat/KM = 1.34 mM-1 s-1) compared to the enzymatic hydrolysis of barley b-D-glucan (KM: 0.04 mM, kcat: 0.51 s-1, kcat/KM = 0.08 mM-1 s-1). Moreover, IfCelS12A enzymatic efficacy is stable in hypersaline sodium chlorids (NaCl) solutions (up to 10% NaCl). Specifically, IfCel12A retains notable activity after 24 h at 2M NaCl (10% saline solution). IfCelS12A used as a cocktail component with other cellulolytic enzymes and in conjunction with mobile sequestration platform technology offers additional options for deconstruction of ionic liquid-pretreated cellulosic feedstock. KEY POINTS: • IfCelS12A from an anaerobic alkaliphile Iocasia fronsfrigidae shows salt tolerance • IfCelS12A in cocktails with other enzymes efficiently degrades cellulosic biomass • IfCelS12A used with mobile enzyme sequestration platforms enhances hydrolysis.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chinnapong Wangnai
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road Klong Luang, Pathumthani, 12120, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| | - Ruben Michael Ceballos
- Department of Molecular and Cell Biology, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
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Uttarotai T, McGenity TJ, Sutheeworapong S, Chitov T. Draft genome sequence of Methylobacterium sp. 37f isolated from forest soil. Microbiol Resour Announc 2024:e0032424. [PMID: 38767399 DOI: 10.1128/mra.00324-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
In this study, we report the draft genome sequence data of Methylobacterium sp. 37f, isolated from soil beneath Quercus semiserrata Roxb. in Thailand. The genome consists of 5,305,449 base pairs, with a GC content of 67.5%.
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Affiliation(s)
- Toungporn Uttarotai
- Department of Highland Agriculture and Natural Resources, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Terry J McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Thararat Chitov
- Department of Biology, Faculty of Science, Chiang Mai University, Chaing Mai, Thailand
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Siriatcharanon AK, Sutheeworapong S, Baramee S, Waeonukul R, Pason P, Kosugi A, Uke A, Ratanakhanokchai K, Tachaapaikoon C. Discovery of a Novel Cellobiose Dehydrogenase from Cellulomonas palmilytica EW123 and Its Sugar Acids Production. J Microbiol Biotechnol 2024; 34:457-466. [PMID: 38044713 PMCID: PMC10940743 DOI: 10.4014/jmb.2307.07004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/22/2023] [Accepted: 09/20/2023] [Indexed: 12/05/2023]
Abstract
Cellobiose dehydrogenases (CDHs) are a group of enzymes belonging to the hemoflavoenzyme group, which are mostly found in fungi. They play an important role in the production of acid sugar. In this research, CDH annotated from the actinobacterium Cellulomonas palmilytica EW123 (CpCDH) was cloned and characterized. The CpCDH exhibited a domain architecture resembling class-I CDH found in Basidiomycota. The cytochrome c and flavin-containing dehydrogenase domains in CpCDH showed an extra-long evolutionary distance compared to fungal CDH. The amino acid sequence of CpCDH revealed conservative catalytic amino acids and a distinct flavin adenine dinucleotide region specific to CDH, setting it apart from closely related sequences. The physicochemical properties of CpCDH displayed optimal pH conditions similar to those of CDHs but differed in terms of optimal temperature. The CpCDH displayed excellent enzymatic activity at low temperatures (below 30°C), unlike other CDHs. Moreover, CpCDH showed the highest substrate specificity for disaccharides such as cellobiose and lactose, which contain a glucose molecule at the non-reducing end. The catalytic efficiency of CpCDH for cellobiose and lactose were 2.05 x 105 and 9.06 x 104 (M-1 s-1), respectively. The result from the Fourier-transform infrared spectroscopy (FT-IR) spectra confirmed the presence of cellobionic and lactobionic acids as the oxidative products of CpCDH. This study establishes CpCDH as a novel and attractive bacterial CDH, representing the first report of its kind in the Cellulomonas genus.
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Affiliation(s)
- Ake-kavitch Siriatcharanon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sawannee Sutheeworapong
- Division of Bioinformatics and Systems Biology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sirilak Baramee
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
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4
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Chuaypen N, Asumpinawong A, Sawangsri P, Khamjerm J, Iadsee N, Jinato T, Sutheeworapong S, Udomsawaengsup S, Tangkijvanich P. Gut Microbiota in Patients with Non-Alcoholic Fatty Liver Disease without Type 2 Diabetes: Stratified by Body Mass Index. Int J Mol Sci 2024; 25:1807. [PMID: 38339096 PMCID: PMC10855659 DOI: 10.3390/ijms25031807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The relationship between gut dysbiosis and body mass index (BMI) in non-diabetic patients with non-alcoholic fatty liver disease (NAFLD) is not adequately characterized. This study aimed to assess gut microbiota's signature in non-diabetic individuals with NAFLD stratified by BMI. The 16S ribosomal RNA sequencing was performed for gut microbiota composition in 100 patients with NAFLD and 16 healthy individuals. The differential abundance of bacterial composition between groups was analyzed using the DESeq2 method. The alpha diversity (Chao1, Shannon, and observed feature) and beta diversity of gut microbiota significantly differed between patients with NAFLD and healthy controls. However, significant differences in their diversities were not observed among subgroups of NAFLD. At the phylum level, there was no trend of an elevated Firmicutes/Bacteroidetes ratio according to BMI. At the genus level, patients with lean NAFLD displayed a significant enrichment of Escherichia-Shigella and the depletion of Lachnospira and Subdoligranulum compared to the non-lean subgroups. Combining these bacterial genera could discriminate lean from non-lean NAFLD with high diagnostic accuracy (AUC of 0.82). Non-diabetic patients with lean NAFLD had a significant difference in bacterial composition compared to non-lean individuals. Our results might provide evidence of gut microbiota signatures associated with the pathophysiology and potential targeting therapy in patients with lean NAFLD.
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Affiliation(s)
- Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (N.C.); (J.K.); (N.I.); (T.J.)
- Metabolic Diseases in Gut and Urinary System Research Unit (MeDGURU), Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Aisawan Asumpinawong
- Treatment of Obesity and Metabolic Disease Research Unit, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (A.A.); (P.S.); (S.U.)
| | - Pattarose Sawangsri
- Treatment of Obesity and Metabolic Disease Research Unit, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (A.A.); (P.S.); (S.U.)
| | - Jakkrit Khamjerm
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (N.C.); (J.K.); (N.I.); (T.J.)
- Biomedical Engineering Program, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nutta Iadsee
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (N.C.); (J.K.); (N.I.); (T.J.)
- Medical Biochemistry Program, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thananya Jinato
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (N.C.); (J.K.); (N.I.); (T.J.)
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Research Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand;
| | - Suthep Udomsawaengsup
- Treatment of Obesity and Metabolic Disease Research Unit, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (A.A.); (P.S.); (S.U.)
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (N.C.); (J.K.); (N.I.); (T.J.)
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Suta S, Ophakas S, Manosan T, Honwichit O, Charoensiddhi S, Surawit A, Pongkunakorn T, Pumeiam S, Mongkolsucharitkul P, Pinsawas B, Sutheeworapong S, Puangsombat P, Khoomrung S, Mayurasakorn K. Influence of Prolonged Whole Egg Supplementation on Insulin-like Growth Factor 1 and Short-Chain Fatty Acids Product: Implications for Human Health and Gut Microbiota. Nutrients 2023; 15:4804. [PMID: 38004198 PMCID: PMC10674712 DOI: 10.3390/nu15224804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The gut microbiota exert a profound influence on human health and metabolism, with microbial metabolites playing a pivotal role in shaping host physiology. This study investigated the impact of prolonged egg supplementation on insulin-like growth factor 1 (IGF-1) and circulating short-chain fatty acids (SCFAs). In a subset of a cluster-randomized trial, participants aged 8-14 years were randomly assigned into three groups: (1) Whole Egg (WE)-consuming 10 additional eggs per week [n = 24], (2) Protein Substitute (PS)-consuming yolk-free egg substitute equivalent to 10 eggs per week [n = 25], and (3) Control Group (C) [n = 26]. At week 35, IGF-1 levels in WE significantly increased (66.6 ± 27.7 ng/mL, p < 0.05) compared to C, with positive SCFA correlations, except acetate. Acetate was stable in WE, increasing in PS and C. Significant propionate differences occurred between WE and PS (14.8 ± 5.6 μmol/L, p = 0.010). WE exhibited notable changes in the relative abundance of the Bifidobacterium and Prevotella genera. Strong positive SCFA correlations were observed with MAT-CR-H4-C10 and Libanicoccus, while Roseburia, Terrisporobacter, Clostridia_UCG-014, and Coprococcus showed negative correlations. In conclusion, whole egg supplementation improves growth factors that may be related to bone formation and growth; it may also promote benefits to gut microbiota but may not affect SCFAs.
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Affiliation(s)
- Sophida Suta
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Suphawan Ophakas
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Thamonwan Manosan
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Orranich Honwichit
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (O.H.); (S.C.)
| | - Suvimol Charoensiddhi
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand; (O.H.); (S.C.)
| | - Apinya Surawit
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Tanyaporn Pongkunakorn
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Sureeporn Pumeiam
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Pichanun Mongkolsucharitkul
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Bonggochpass Pinsawas
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Research Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand;
| | - Patcha Puangsombat
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (P.P.); (S.K.)
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (P.P.); (S.K.)
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Korapat Mayurasakorn
- Siriraj Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (S.S.); (S.O.); (T.M.); (A.S.); (T.P.); (S.P.); (P.M.); (B.P.)
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Leelastwattanagul O, Sutheeworapong S, Khoiri AN, Dulsawat S, Wattanachaisaereekul S, Tachaleat A, Duangfoo T, Paenkaew P, Prommeenate P, Cheevadhanarak S, Jirakkakul J. Soil microbiome analysis reveals effects of periodic waterlogging stress on sugarcane growth. PLoS One 2023; 18:e0293834. [PMID: 37917788 PMCID: PMC10621937 DOI: 10.1371/journal.pone.0293834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
Sugarcane is one of the major agricultural crops with high economic importance in Thailand. Periodic waterlogging has a long-term negative effect on sugarcane development, soil properties, and microbial diversity, impacting overall sugarcane production. Yet, the microbial structure in periodically waterlogged sugarcane fields across soil compartments and growth stages in Thailand has not been documented. This study investigated soil and rhizosphere microbial communities in a periodic waterlogged field in comparison with a normal field in a sugarcane plantation in Ratchaburi, Thailand, using 16S rRNA and ITS amplicon sequencing. Alpha diversity analysis revealed comparable values in periodic waterlogged and normal fields across all growth stages, while beta diversity analysis highlighted distinct microbial community profiles in both fields throughout the growth stages. In the periodic waterlogged field, the relative abundance of Chloroflexi, Actinobacteria, and Basidiomycota increased, while Acidobacteria and Ascomycota decreased. Beneficial microbes such as Arthrobacter, Azoarcus, Bacillus, Paenibacillus, Pseudomonas, and Streptomyces thrived in the normal field, potentially serving as biomarkers for favorable soil conditions. Conversely, phytopathogens and growth-inhibiting bacteria were prevalent in the periodic waterlogged field, indicating unfavorable conditions. The co-occurrence network in rhizosphere of the normal field had the highest complexity, implying increased sharing of resources among microorganisms and enhanced soil biological fertility. Altogether, this study demonstrated that the periodic waterlogged field had a long-term negative effect on the soil microbial community which is a key determining factor of sugarcane growth.
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Affiliation(s)
- Onnicha Leelastwattanagul
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Ahmad Nuruddin Khoiri
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- School of Food Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Thanawat Duangfoo
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Prasobsook Paenkaew
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
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Wongsurawat T, Sutheeworapong S, Jenjaroenpun P, Charoensiddhi S, Khoiri AN, Topanurak S, Sutthikornchai C, Jintaridth P. Microbiome analysis of thai traditional fermented soybeans reveals short-chain fatty acid-associated bacterial taxa. Sci Rep 2023; 13:7573. [PMID: 37165206 PMCID: PMC10172314 DOI: 10.1038/s41598-023-34818-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
Thua Nao is a Thai traditional fermented soybean food and low-cost protein supplement. This study aimed to evaluate the bacterial community in Thua Nao from northern Thailand and assess potentially active short-chain fatty acids (SCFAs)-related bacteria. Sixty-five Thua Nao consisting of 30 wet and 35 dried samples were collected from six provinces: Chiang Rai, Chiang Mai, Mae Hong Son, Lampang, Lamphun, and Phayao. Bacterial diversity was significantly higher in the wet samples than in the dried samples. The dominant phyla were Firmicutes (92.7%), Proteobacteria (6.7%), Actinobacteriota (0.42%), and Bacteroidota (0.26%). The genus Bacillus (67%) was the most represented in all samples. Lactobacillus, Enterococcus, and Globicatella were enriched in the wet samples. Assessment of the SCFA-microbiota relationships revealed that high butyrate and propionate concentrations were associated with an increased Clostridiales abundance, and high acetate concentrations were associated with an increased Weissella abundance. Wet products contained more SCFAs, including acetate (P = 2.8e-08), propionate (P = 0.0044), butyrate (P = 0.0021), and isovalerate (P = 0.017), than the dried products. These results provide insight into SCFA-microbiota associations in Thua Nao, which may enable the development of starter cultures for SCFA-enriched Thua Nao production.
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Affiliation(s)
- Thidathip Wongsurawat
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Bangkok, 10700, Thailand.
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Long-Read Lab (Si-LoL), Faculty of Medicine Siriraj Hospital, Bangkok, 10700, Thailand
| | - Suvimol Charoensiddhi
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok, 10900, Thailand
| | - Ahmad Nuruddin Khoiri
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Supachai Topanurak
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Chantira Sutthikornchai
- Department of Protozoology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Pornrutsami Jintaridth
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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8
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Suta S, Surawit A, Mongkolsucharitkul P, Pinsawas B, Manosan T, Ophakas S, Pongkunakorn T, Pumeiam S, Sranacharoenpong K, Sutheeworapong S, Poungsombat P, Khoomrung S, Akarasereenont P, Thaipisuttikul I, Suktitipat B, Mayurasakorn K. Prolonged Egg Supplement Advances Growing Child's Growth and Gut Microbiota. Nutrients 2023; 15:nu15051143. [PMID: 36904143 PMCID: PMC10005095 DOI: 10.3390/nu15051143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Protein-energy malnutrition still impacts children's growth and development. We investigated the prolonged effects of egg supplementation on growth and microbiota in primary school children. For this study, 8-14-year-old students (51.5% F) in six rural schools in Thailand were randomly assigned into three groups: (1) whole egg (WE), consuming 10 additional eggs/week (n = 238) (n = 238); (2) protein substitute (PS), consuming yolk-free egg substitutes equivalent to 10 eggs/week (n = 200); and (3) control group (C, (n = 197)). The outcomes were measured at week 0, 14, and 35. At the baseline, 17% of the students were underweight, 18% were stunted, and 13% were wasted. At week 35, compared to the C group the weight and height difference increased significantly in the WE group (3.6 ± 23.5 kg, p < 0.001; 5.1 ± 23.2 cm, p < 0.001). No significant differences in weight or height were observed between the PS and C groups. Significant decreases in atherogenic lipoproteins were observed in the WE, but not in PS group. HDL-cholesterol tended to increase in the WE group (0.02 ± 0.59 mmol/L, ns). The bacterial diversity was similar among the groups. The relative abundance of Bifidobacterium increased by 1.28-fold in the WE group compared to the baseline and differential abundance analysis which indicated that Lachnospira increased and Varibaculum decreased significantly. In conclusion, prolonged whole egg supplementation is an effective intervention to improve growth, nutritional biomarkers, and gut microbiota with unaltered adverse effects on blood lipoproteins.
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Affiliation(s)
- Sophida Suta
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Apinya Surawit
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pichanun Mongkolsucharitkul
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Bonggochpass Pinsawas
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thamonwan Manosan
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Suphawan Ophakas
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Tanyaporn Pongkunakorn
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sureeporn Pumeiam
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | | | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Research Unit, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Patcha Poungsombat
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pravit Akarasereenont
- Department of Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Iyarit Thaipisuttikul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Bhoom Suktitipat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Korapat Mayurasakorn
- Population Health and Nutrition Research Group, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Correspondence: ; Tel.: +66-9-4189-3266
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9
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Heng S, Sutheeworapong S, Champreda V, Uke A, Kosugi A, Pason P, Waeonukul R, Ceballos RM, Ratanakhanokchai K, Tachaapaikoon C. Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation. PeerJ 2022; 10:e14211. [PMID: 36281362 PMCID: PMC9587714 DOI: 10.7717/peerj.14211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/19/2022] [Indexed: 01/24/2023] Open
Abstract
Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1T. Prior to characterization of strain NS-1T, an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae. Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1T. In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons (e.g., 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1T, strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1T. Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1T. The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Ruben Michael Ceballos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America,Arkansas Center for Space & Planetary Sciences, University of Arkansas, Fayetteville, AR, United States of America
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
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10
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Siriatcharanon AK, Sutheeworapong S, Waeonukul R, Pason P, Uke A, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C. Erratum: Cellulomonas palmilytica sp. nov., from earthworm soil biofertilizer with potential to degrade oil palm empty fruit bunch. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Ake-kavitch Siriatcharanon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Khanok Ratanakhanokchai
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
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11
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Siriatcharanon AK, Sutheeworapong S, Waeonukul R, Pason P, Uke A, Kosugi A, Ratanakhanokchai K, Tachaapaikoon C. Cellulomonas palmilyticum sp. nov., from earthworm soil biofertilizer with the potential to degrade oil palm empty fruit bunch. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oil palm empty fruit bunch (OPEFB) is lignocellulosic waste from the palm oil industry in Southeast Asia. It is difficult to degrade because of its complex matrix and recalcitrant structure. To decompose OPEFB, highly efficient micro-organisms and robust enzymatic systems are required. A bacterium with high degradation ability against untreated OPEFB was isolated from earthworm soil biofertilizer and designated as strain EW123T. Cells were Gram-stain-positive, rod-shaped and catalase-positive. In tests, the strain was negative for mycelium formation, motility, nitrate reductase and urease. The 16S rRNA gene analysis of the isolate showed 98.21 % similarity to
Cellulomonas uda
NBRC 3747T, whereas similarity to other species was below 98 %. The genome of strain EW123T was 3 834 009 bp long, with 73.97 mol% G+C content. Polar lipid analysis of strain EW123T indicated phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and aminophospholipid as the lipid components of the cell wall. The major cellular fatty acid was anteiso-C15 : 0 (41.26 %) and the isomer of 2,6-diaminopimelic acid (DAP) was meso-DAP. The average nucleotide identity value between the genome sequences of EW123T and
C. uda
NBRC 3747T was 88.6 %. In addition, the digital DNA–DNA hybridization and genome average amino acid between those strains were 36.1 and 89.68 %, respectively. The ORF number (186) of carbohydrate-active enzymes, including cellulases, xylanases, mannanase, lipase and lignin-degrading enzymes, was higher than those of related strains. These results indicate that the polyphasic characteristics of EW123T differ from those of other related species in the genus
Cellulomonas
. We therefore propose a novel species of the genus
Cellulomonas
, namely Cellulomonas palmilyticum sp. nov. (type strain TBRC 11805T=NBRC 114552T), with the ability to effectively degrade untreated OPEFB.
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Affiliation(s)
- Ake-kavitch Siriatcharanon
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Laboratory, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Khanok Ratanakhanokchai
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Chakrit Tachaapaikoon
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10150, Thailand
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12
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Cherdtrakulkiat T, Wongsurawat T, Jenjaroenpun P, Sutheeworapong S, Leelawiwat W, Woodring JV, Dunne EF, Papp JR, Srifuengfung S, Tribuddharat C. Complete Genome Sequence of Neisseria gonorrhoeae Multilocus Sequence Type ST7363 Isolated from Thailand. Microbiol Resour Announc 2021; 10:e0057321. [PMID: 34647806 PMCID: PMC8515890 DOI: 10.1128/mra.00573-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
A Neisseria gonorrhoeae multilocus sequence type (MLST) ST7363 strain was isolated from a patient at the Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand, in 2010 and completely sequenced. This strain is susceptible to ceftriaxone and cefixime. A complete circular chromosome and circular plasmids were assembled from combined Oxford Nanopore Technologies (ONT) and Illumina sequencing.
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Affiliation(s)
- Thitima Cherdtrakulkiat
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wanna Leelawiwat
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Joseph V. Woodring
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Eileen F. Dunne
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - John R. Papp
- Division of Sexually Transmitted Disease Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Chanwit Tribuddharat
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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13
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Cheawchanlertfa P, Tongsuk P, Sutheeworapong S, Waeonukul R, Pason P, Poomputsa K, Ratanakhanokchai K, Kosugi A, Tachaapaikoon C. A novel amylolytic/xylanolytic/cellulolytic multienzyme complex from Clostridium manihotivorum that hydrolyzes polysaccharides in cassava pulp. Appl Microbiol Biotechnol 2021; 105:6719-6733. [PMID: 34436648 DOI: 10.1007/s00253-021-11521-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 11/30/2022]
Abstract
Some anaerobic bacteria, particularly Clostridium species, produce extracellular cellulolytic and xylanolytic enzymes as multienzyme complexes (MECs). However, an amylolytic/xylanolytic/cellulolytic multienzyme complex (AXC-MEC) from anaerobic bacteria is rarely found. In this work, the glycoprotein AXC-MEC, composed of subunits of amylolytic, xylanolytic, and cellulolytic enzymes, was isolated from crude extracellular enzyme of the mesophilic anaerobic bacterium Clostridium manihotivorum CT4, grown on cassava pulp, using a milled cassava pulp column and Sephacryl S-500 gel filtration chromatography. The isolated AXC-MEC showed a single band upon native-polyacrylamide gel electrophoresis (native-PAGE). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed at least eight protein bands of the multienzyme complex which predominantly exhibited amylolytic enzyme activity, followed by xylanolytic and cellulolytic enzyme activities. The AXC-MEC is highly capable of degrading starch and non-starch polysaccharides present in cassava pulp into glucose and oligosaccharides, without conventional pretreatment. Base on the genomic analysis of C. manihotivorum CT4, we found no evidence of the known structural components of the well-known multienzyme complexes from Clostridium species, cellulosomes such as scaffoldin, cohesin, and dockerin, indicating that AXC-MEC from strain CT4 exhibit a different manner of assembly from the cellulosomes. These results suggest that AXC-MEC from C. manihotivorum CT4 is a new MEC capable of hydrolyzing cassava pulp into value-added products, which will benefit the starch industry. KEY POINTS: • Glycoprotein AXC-MEC was first reported in Clostridium manihotivorum. • Unlike cellulosomes, AXC-MEC consists of amylase, xylanase, and cellulase. • Glucose and oligosaccharides were hydrolysis products from cassava pulp by AXC-MEC.
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Affiliation(s)
- Pattsarun Cheawchanlertfa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Pornpimon Tongsuk
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Sawannee Sutheeworapong
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Kanokwan Poomputsa
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand. .,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
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14
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Thongsamer T, Neamchan R, Blackburn A, Acharya K, Sutheeworapong S, Tirachulee B, Pattanachan P, Vinitnantharat S, Zhou XY, Su JQ, Zhu YG, Graham D, Werner D. Environmental antimicrobial resistance is associated with faecal pollution in Central Thailand's coastal aquaculture region. J Hazard Mater 2021; 416:125718. [PMID: 33857807 DOI: 10.1016/j.jhazmat.2021.125718] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
We assessed antimicrobial resistance (AMR) potential to seven major classes of antibiotics in Central Thailand's coastal aquaculture region using high-throughput qPCR targeting 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). In parallel, we used MinION next generation sequencing (NGS) of 16S rRNA gene amplicons, qPCR of faecal pollution makers, and conventional plate count methods for the comprehensive characterization of environmental microbiomes. We tested the hypothesis that aquaculture increases environmental AMR by comparing ARGs and MGEs in water and sediment samples from five aquaculture sites and their associated canals. There was no evidence from the ARG and MGE data that aquaculture is a major driver of environmental AMR in Central Thailand. Instead, the highest relative prevalence of resistance traits was found in Hua Krabue canal water influenced by urban pollution from Bangkok at the inland edge of the coastal aquaculture region. The sum of ARGs and MGEs, relative to 16S rRNA genes used as markers for overall bacterial abundance, was between 0.495 ± 0.011 and 0.498 ± 0.013 in Hua Krabue canal water, compared with at most 0.132 ± 0.005 in all the other environmental samples. Corresponding patterns were observed for most faecal pollution markers, which were also elevated in Hua Krabue canal water.
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Affiliation(s)
- Thunchanok Thongsamer
- Environmental Technology Program, School of Energy, Environment and Materials, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Rattikan Neamchan
- Environmental Technology Program, School of Energy, Environment and Materials, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Adrian Blackburn
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Bundit Tirachulee
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Pavinee Pattanachan
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Soydoa Vinitnantharat
- Environmental Technology Program, School of Energy, Environment and Materials, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Xin-Yuan Zhou
- Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Jian-Qiang Su
- Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - Yong-Guan Zhu
- Institute of Urban Environment, Chinese Academy of Science, Xiamen 361021, China
| | - David Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom.
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15
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Khoiri AN, Cheevadhanarak S, Jirakkakul J, Dulsawat S, Prommeenate P, Tachaleat A, Kusonmano K, Wattanachaisaereekul S, Sutheeworapong S. Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. Front Microbiol 2021; 12:623799. [PMID: 33828538 PMCID: PMC8019924 DOI: 10.3389/fmicb.2021.623799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.
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Affiliation(s)
- Ahmad Nuruddin Khoiri
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jiraporn Jirakkakul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Sudarat Dulsawat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Anuwat Tachaleat
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Kanthida Kusonmano
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Songsak Wattanachaisaereekul
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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16
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Cheawchanlertfa P, Sutheeworapong S, Jenjaroenpun P, Wongsurawat T, Nookaew I, Cheevadhanarak S, Kosugi A, Pason P, Waeonukul R, Ratanakhanokchai K, Tachaapaikoon C. Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. PeerJ 2020; 8:e10343. [PMID: 33240652 PMCID: PMC7676355 DOI: 10.7717/peerj.10343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/20/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. METHODS A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. RESULTS Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).
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Affiliation(s)
- Pattsarun Cheawchanlertfa
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
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17
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Intarajak T, Udomchaiprasertkul W, Bunyoo C, Yimnoon J, Soonklang K, Wiriyaukaradecha K, Lamlertthon W, Sricharunrat T, Chaiwiriyawong W, Siriphongpreeda B, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Jenjaroenpun P, Wongsurawat T, Nookaew I, Auewarakul C, Cheevadhanarak S. Genetic Aberration Analysis in Thai Colorectal Adenoma and Early-Stage Adenocarcinoma Patients by Whole-Exome Sequencing. Cancers (Basel) 2019; 11:E977. [PMID: 31336886 PMCID: PMC6679221 DOI: 10.3390/cancers11070977] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal adenomas are precursor lesions of colorectal adenocarcinoma. The transition from adenoma to carcinoma in patients with colorectal cancer (CRC) has been associated with an accumulation of genetic aberrations. However, criteria that can screen adenoma progression to adenocarcinoma are still lacking. This present study is the first attempt to identify genetic aberrations, such as the somatic mutations, copy number variations (CNVs), and high-frequency mutated genes, found in Thai patients. In this study, we identified the genomic abnormality of two sample groups. In the first group, five cases matched normal-colorectal adenoma-colorectal adenocarcinoma. In the second group, six cases matched normal-colorectal adenomas. For both groups, whole-exome sequencing was performed. We compared the genetic aberration of the two sample groups. In both normal tissues compared with colorectal adenoma and colorectal adenocarcinoma analyses, somatic mutations were observed in the tumor suppressor gene APC (Adenomatous polyposis coli) in eight out of ten patients. In the group of normal tissue comparison with colorectal adenoma tissue, somatic mutations were also detected in Catenin Beta 1 (CTNNB1), Family With Sequence Similarity 123B (FAM123B), F-Box And WD Repeat Domain Containing 7 (FBXW7), Sex-Determining Region Y-Box 9 (SOX9), Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5), Frizzled Class Receptor 10 (FZD10), and AT-Rich Interaction Domain 1A (ARID1A) genes, which are involved in the Wingless-related integration site (Wnt) signaling pathway. In the normal tissue comparison with colorectal adenocarcinoma tissue, Kirsten retrovirus-associated DNA sequences (KRAS), Tumor Protein 53 (TP53), and Ataxia-Telangiectasia Mutated (ATM) genes are found in the receptor tyrosine kinase-RAS (RTK-RAS) signaling pathway and p53 signaling pathway, respectively. These results suggest that APC and TP53 may act as a potential screening marker for colorectal adenoma and early-stage CRC. This preliminary study may help identify patients with adenoma and early-stage CRC and may aid in establishing prevention and surveillance strategies to reduce the incidence of CRC.
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Affiliation(s)
- Thoranin Intarajak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Bioinformatics Unit for Genomic Analysis, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Wandee Udomchaiprasertkul
- Molecular Biology and Genomic Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Chakrit Bunyoo
- Bioinformatics Unit for Genomic Analysis, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Jutamas Yimnoon
- Cytogenetics Unit, Central Research Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kamonwan Soonklang
- Data Management Unit, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Kriangpol Wiriyaukaradecha
- Molecular Biology and Genomic Laboratory, Division of Research and International Relations, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Wisut Lamlertthon
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Thaniya Sricharunrat
- Pathology Laboratory Unit, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Worawit Chaiwiriyawong
- Department of Medical Oncology, Chulabhorn Hospital, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Bunchorn Siriphongpreeda
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Sawannee Sutheeworapong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Weerayuth Kittichotirat
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Systems Biology research group, National Center for Genetic Engineering and Biotechnology (BIOTEC) at King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department of Physiology and Biophysics, College of Medicine, The University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Chirayu Auewarakul
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok 10210, Thailand.
| | - Supapon Cheevadhanarak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
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18
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Jenjaroenpun P, Wongsurawat T, Sutheeworapong S, Kuznetsov VA. R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. Nucleic Acids Res 2017; 45:D119-D127. [PMID: 27899586 PMCID: PMC5210542 DOI: 10.1093/nar/gkw1054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 10/04/2016] [Accepted: 10/20/2016] [Indexed: 11/18/2022] Open
Abstract
R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1 565 795 RLFSs distributed in 121 056 genic or proximal gene regions of the covered organisms. It provides a comprehensive annotation of Ensembl RLFS-positive genes including 93 454 protein coding genes, 12 480 long non-coding RNA and 7 568 small non-coding RNA genes and 7 554 pseudogenes. Using new interface and genome viewers of R-loopDB, users can search the gene(s) in multiple species with keywords in a single query. R-loopDB provides tools to carry out comparative evolution and genome-scale analyses in R-loop biology.
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Affiliation(s)
- Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, 138671, Singapore
| | - Thidathip Wongsurawat
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, 138671, Singapore
| | - Sawannee Sutheeworapong
- Systems Biology and Bioinformatics Research, Pilot Plant Development and Training Institute, King Mongkut's University of Technology, Thonburi, Bangkok, Thailand
| | - Vladimir A Kuznetsov
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, 138671, Singapore
- School of Computer Engineering, Nanyang Technological University, 639798, Singapore
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Panyakampol J, Cheevadhanarak S, Sutheeworapong S, Chaijaruwanich J, Senachak J, Siangdung W, Jeamton W, Tanticharoen M, Paithoonrangsarid K. Physiological and Transcriptional Responses to High Temperature in Arthrospira ( Spirulina ) platensis C1. ACTA ACUST UNITED AC 2014; 56:481-96. [DOI: 10.1093/pcp/pcu192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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20
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Abstract
OBJECTIVE With the dramatic increase in microarray data, biclustering has become a promising tool for gene expression analysis. Biclustering has been proven to be superior over clustering in identifying multifunctional genes and searching for co-expressed genes under a few specific conditions; that is, a subgroup of all conditions. Biclustering based on a genetic algorithm (GA) has shown better performance than greedy algorithms, but the overlap state for biclusters must be treated more systematically. RESULTS We developed a new biclustering algorithm (binary-iterative genetic algorithm [BIGA]), based on an iterative GA, by introducing a novel, ternary-digit chromosome encoding function. BIGA searches for a set of biclusters by iterative binary divisions that allow the overlap state to be explicitly considered. In addition, the average of the Pearson's correlation coefficient was employed to measure the relationship of genes within a bicluster, instead of the mean square residual, the popular classical index. As compared to the six existing algorithms, BIGA found highly correlated biclusters, with large gene coverage and reasonable gene overlap. The gene ontology (GO) enrichment showed that most of the biclusters are significant, with at least one GO term over represented. CONCLUSION BIGA is a powerful tool to analyze large amounts of gene expression data, and will facilitate the elucidation of the underlying functional mechanisms in living organisms.
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Affiliation(s)
- Sawannee Sutheeworapong
- Department of Biological Sciences, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
- Graduate School of Information Sciences, Tohoku University, Miyagi, Japan
| | - Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Nagoya, Japan
| | - Hiroyuki Ohta
- Department of Biological Sciences, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kengo Kinoshita
- Graduate School of Information Sciences, Tohoku University, Miyagi, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan
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