Different allergic phenotypes exhibit unique patterns of gut microbiota from early life Anchalee Senavonge 1, Massalin Nakphaichit2,3, Wanwipa Vongsangnak 4,5, Sittiruk Roytrakul 6, Preecha Patumcharoenpol7, Amornthep Kingkaw 7, Chantha Wongoutong 8, Wanlapa Weerapakorn 1, Natapol Pornputtapong 9,10, Orawan La-ongkham11, Pannipa Kittipongpattana 1, Sunee Nitisinprasert 4,5, Pantipa Chatchatee1*, Narissara Suratannon 1*1 Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand2 Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand3 Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand4 Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand5 Specialized Research Unit: Probiotics and Prebiotics for Health, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand6 Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand7 Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand8 Department of Statistics, Faculty of Science, Kasetsart University, Bangkok, Thailand9 Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand10 Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand11 Department of Applied Microbiology, Institute of Food Research and Product Development, Kasetsart University, Bangkok, Thailand* Corresponding author:Narissara Suratannon, MDPediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand1873, Praram 4 Road, Pathumwan, Bangkok, 10330, ThailandTel: +662 256 4951E-mail: narissara.su@chula.md, orchid number: 0000-0003-1182-3611Pantipa Chatchatee, MDPediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand1873, Praram 4 Road, Pathumwan, Bangkok, 10330, ThailandTel: +662 256 4971E-mail: pantipa.c@chula.md* Pantipa Chatchatee and Narissara Suratannon are considered joint corresponding authors.Keywords: proteomics, gastrointestinal microbiome, cohort studies, dermatitis, atopic, food hypersensitivityFunding sources: This study was supported by National Science and Technology Development Agency (NSTDA) (Grant No. P-17-50648), Ratchadapisek Research Funds (Grant No. CU-GR(S)_61_38_30_03), Chulalongkorn University, Bangkok, Thailand.Conflicts of interest: All authors have no relevant financial relationships to disclose.Authors’ contributions: AS contributed on writing the first draft of manuscript, data collection and data analysis; WV and PP performed bioinformatic analysis and wrote the manuscript, MN performed 16S sequencing, real-time PCR and wrote the manuscript, AK and SR performed proteomic analysis and wrote the manuscript. CW performed the statistical analysis and wrote the manuscript. WW, NP, OL, PK and SN provided valuable advice, reviewed and edited the manuscript. PC and NS wrote the manuscript and taking care overall of this work. All authors read and approved the final manuscript.Ethics approval: The study was approved by the Ethics Committee of King Chulalongkorn Memorial Hospital in Bangkok, Thailand (IRB No. 358/58).Abbreviations: AD: atopic dermatitis, FA: food allergyAcknowledgments: The authors would like to thank pediatric allergists and research team from Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand and Center of Excellence Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand especially Professor Yong Poovorawan, Dr. Nasamon Wanlapakorn for enrollment, follow-up the subjects and collected stool samples in this cohort. We would also like to thank the Department of Zoology, International SciKU Branding (ISB), Faculty of Science, Kasetsart University, Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU) and SciKU Biodata Server for resources and computing facilities. We also would like to thank Prof. Jarungchit Ngamphaiboon from Chulalongkorn University for valuable comments and suggestions.Word count 594 words; 1 figure, 1 tableData Deposition: Sequence data generated and analyzed during this study are available on the NIH Sequence Read Archive (SRA) under Bioproject ID PRJNA716451. Raw MS/MS spectra data are available in ProteomeXchange: JPST001282 and PXD027692.To the editor,Allergic diseases are known to be associated with gut dysbiosis. However, whether gut microbial colonization and functions are different among distinct allergic phenotypes has not been elucidated. This study aimed to identify differences in gut microbiota between healthy subjects, subjects with only atopic dermatitis (AD), or food allergy (FA), or those with both AD and FA (AD+FA), using 16s rRNA sequencing and shotgun metaproteomic approach. Study populations were derived from a longitudinal birth cohort in Bangkok, Thailand, conducted during 2015 and 2019. Fecal samples of 26 allergic subjects and 26 matched controls were collected at age 9-12 months. Demographic data were shown in Table S1.Compared to controls, gut microbiome of allergic subjects showed a trend of decreased bacterial diversity and richness. This trend was most pronounced in FA (Figure 1A). The diversity of AD and AD+FA were not different compared to controls. No significant clustering was found among samples within groups (Figure S1). Regarding microbiome composition (Figure 1B), subjects with AD and AD+FA were significantly colonized with Erysipelotrichaceae . FA and AD+FA groups had low abundance of Bifidobacteriaceae but high abundance ofBacteroidaceae . Enterobacteriaceae was prominently found in FA. Microbiome profiling using real-time PCR confirmed the findings of 16S rRNA gene sequencing (Figure S2).Using metaproteome analysis, 37,579 microbial protein expressions from 12 bacterial families were identified in all subjects (Figure 1C), in which 1,179 differentially expressed proteins (DEPs) were observed between four study groups. Interestingly, all DEPs were higher in allergic subjects than controls (Figure S4). Subjects with AD+FA showed the highest distinctive DEPs, followed by FA and AD (Figure 1D). This reflected that the microbial functions of the AD+FA group were more deviate from healthy subjects than those with only AD or FA. Notably, DEPs of AD+FA and FA groups were similar, while a large difference between AD+FA and AD was observed. This implied that bacterial metabolic activities in the AD+FA group were more similar to FA than the AD group.By manual curation, 37 proteins from 4 bacterial families found from 16S bacterial sequencing were selected and functionally assigned (Table 1). In AD+FA group, proteins involving thiamine, riboflavin and menaquinone synthesis were found from three genera of Enterobacteriaceae . Proteins involving in carbohydrate metabolism were found inBifidobacterium pseudocatenulatum, Enterobacter huaxiensis, Enterobacter cloacae, Escherichia coli and Faecalitalea cylindroides , reflecting high activities of these gut microbiome. In AD group, a protein involving menaquinone synthesis demethylmenaquinone methyltransferase (DMM) from Bacteroides sp. ,and 6-phospho-beta-glucosidase from Erysipelotrichaceae were identified. Finally, proteins involving in pyruvate kinase pathway from Bifidobacterium longum subsp.longum were identified in FA group.From previous studies, Erysipelotrichaceae was reported in inflammatory bowel diseases 1, colorectal cancer2 and type 2 diabetes 3. Our cohort was the first to describe Erysipelotrichaceae related to AD4 and AD+FA phenotypes. Menaquinone (vitamin K2) synthesis pathway was highlighted in AD and AD+FA groups. Previous studies showed that menaquinone was solely produced by gut microbiome and had immunosuppressive effects on peripheral blood of AD subjects5. We hypothesize that menaquinone-producing pathway of gut microbiota is activated to counteract allergic inflammation of human host. This compensatory mechanism might also be the case forBifidobacterium longum, a good bacteria found in FA.Additionally, we confirmed the findings of Bifidobacterium pseudocatenulum in children with AD 6. Finally,Enterobacter cloacae and Faecalitalea cylindroides , which were reported in obesity 7 and Crohn disease8, were first reported in allergic diseases in our cohort.In conclusion, subjects with different allergic phenotypes showed distinct gut microbial patterns and functions. Subjects with both allergic phenotypes (AD+FA) displayed the mixtures pattern but were dominated by the FA pattern.