1
|
Gryaznova M, Smirnova Y, Burakova I, Morozova P, Nesterova E, Gladkikh M, Mikhaylov E, Syromyatnikov M. Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing. Animals (Basel) 2023; 13:2303. [PMID: 37508080 PMCID: PMC10376196 DOI: 10.3390/ani13142303] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Diarrhea in piglets is one of the most common diseases leading to high mortality and, as a result, to economic losses. Shotgun metagenomic sequencing was performed on the DNBSEQ-G50, MGI system to study the role of the fecal microbiome in the development of diarrhea in newborn piglets. Analysis of the study data showed that the composition of the fecal microbiome at the level of bacteria and fungi did not differ in piglets with diarrhea from the healthy group. Bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most abundant. However, a higher level of bacterial alpha diversity was observed in the group of piglets with diarrhea, which may be due to dysbacteriosis and inflammation. The study of the virome showed the difference between the two types of phages: Bacteroides B40-8 prevailed in diseased piglets, while Escherichia virus BP4 was found in greater numbers in healthy piglets. The results of our study suggest that the association between the fecal microbiome and susceptibility to diarrhea in suckling piglets may have been previously overestimated.
Collapse
Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Polina Morozova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Ekaterina Nesterova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gladkikh
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Evgeny Mikhaylov
- FSBSI All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, 394061 Voronezh, Russia
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- FSBSI All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, 394061 Voronezh, Russia
| |
Collapse
|
2
|
Zubeldia-Varela E, Barker-Tejeda TC, Mera-Berriatua L, Bazire R, Cabrera-Freitag P, Ubeda C, Barber D, Francino MP, Rojo D, Ibáñez-Sandín MD, Pérez-Gordo M. Further Insights into the Gut Microbiota of Cow's Milk Allergic Infants: Analysis of Microbial Functionality and Its Correlation with Three Fecal Biomarkers. Int J Mol Sci 2023; 24:ijms24119247. [PMID: 37298198 DOI: 10.3390/ijms24119247] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Cow's milk allergy (CMA) is one of the most prevalent food allergies in children. Several studies have demonstrated that gut microbiota influences the acquisition of oral tolerance to food antigens at initial stages of life. Changes in the gut microbiota composition and/or functionality (i.e., dysbiosis) have been linked to inadequate immune system regulation and the emergence of pathologies. Moreover, omic sciences have become an essential tool for the analysis of the gut microbiota. On the other hand, the use of fecal biomarkers for the diagnosis of CMA has recently been reviewed, with fecal calprotectin, α-1 antitrypsin, and lactoferrin being the most relevant. This study aimed at evaluating functional changes in the gut microbiota in the feces of cow's milk allergic infants (AI) compared to control infants (CI) by metagenomic shotgun sequencing and at correlating these findings with the levels of fecal biomarkers (α-1 antitrypsin, lactoferrin, and calprotectin) by an integrative approach. We have observed differences between AI and CI groups in terms of fecal protein levels and metagenomic analysis. Our findings suggest that AI have altered glycerophospholipid metabolism as well as higher levels of lactoferrin and calprotectin that could be explained by their allergic status.
Collapse
Affiliation(s)
- Elisa Zubeldia-Varela
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
| | - Tomás Clive Barker-Tejeda
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
| | - Leticia Mera-Berriatua
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
| | - Raphaëlle Bazire
- Department of Allergy, H. Infantil Universitario Niño Jesús, FibHNJ, ARADyAL-RETICs Instituto de Salud Carlos III, IIS-P, 28031 Madrid, Spain
| | - Paula Cabrera-Freitag
- Allergy Paediatric Unit, Allergy Service, Hospital General Universitario Gregorio Marañón, Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain
| | - Carles Ubeda
- Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO), 46020 Valencia, Spain
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
| | - Domingo Barber
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
| | - María Pilar Francino
- CIBER en Epidemiología y Salud Pública, 28029 Madrid, Spain
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO) and Institut de Biologia Integrativa de Sistemes (Universitat de València/Consejo Superior de Investigaciones Científicas), Avda. Catalunya 21, 46020 València, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
| | - María Dolores Ibáñez-Sandín
- Department of Allergy, H. Infantil Universitario Niño Jesús, FibHNJ, ARADyAL-RETICs Instituto de Salud Carlos III, IIS-P, 28031 Madrid, Spain
| | - Marina Pérez-Gordo
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
| |
Collapse
|
3
|
Wilson NG, Hernandez-Leyva A, Schwartz DJ, Bacharier LB, Kau AL. The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. bioRxiv 2023:2023.01.03.522677. [PMID: 36711684 PMCID: PMC9882014 DOI: 10.1101/2023.01.03.522677] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Asthma is a common allergic airway disease that develops in association with the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in children and adults 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. One differentially abundant ARG was a macrolide resistance marker, ermF, which significantly co-occurred with the Bacteroides fragilis toxin, suggesting a possible relationship between enterotoxigenic B. fragilis, antibiotic resistance, and asthma. Lastly, we found multiple virulence factor (VF) and ARG pairs that co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are co-selected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.
Collapse
Affiliation(s)
- Naomi G. Wilson
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ariel Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Drew J. Schwartz
- Division of Infectious Diseases, Department of Pediatrics and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leonard B. Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Monroe Carell Jr Children’s Hospital at Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew L. Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| |
Collapse
|
4
|
Schuele L, Lizarazo-Forero E, Strutzberg-Minder K, Schütze S, Löbert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N. Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region. Transbound Emerg Dis 2021; 69:2306-2319. [PMID: 34347385 PMCID: PMC9540031 DOI: 10.1111/tbed.14249] [Citation(s) in RCA: 3] [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: 04/06/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next‐generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch–German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In‐depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens.
Collapse
Affiliation(s)
- Leonard Schuele
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Sabine Schütze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Sandra Löbert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Jürgen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| |
Collapse
|
5
|
Schuele L, Lizarazo-Forero E, Cassidy H, Strutzberg-Minder K, Boehmer J, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N. First detection of porcine respirovirus 1 in Germany and the Netherlands. Transbound Emerg Dis 2021; 68:3120-3125. [PMID: 33837672 PMCID: PMC9292642 DOI: 10.1111/tbed.14100] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 11/10/2020] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 01/10/2023]
Abstract
Porcine respirovirus 1, also referred to as porcine parainfluenza virus 1 (PPIV‐1), was first detected in deceased pigs from Hong Kong in 2013. It has since then been found in the USA, Chile and most recently in Hungary. Information on the pathogenicity and global spread is sparse. However, it has been speculated to play a role in the porcine respiratory disease complex. To investigate the porcine virome, we screened 53 pig samples from 26 farms within the Dutch–German border region using shotgun metagenomics sequencing (SMg). After detecting PPIV‐1 in five farms through SMg, a real‐time reverse transcriptase PCR (RT‐qPCR) assay was designed, which not only confirmed the presence of the virus in 1 of the 5 farms but found an additional 6 positive farms. Phylogenetic analysis found the closest match to be the first detected PPIV‐1 strain in Hong Kong. The Dutch‐German region represents a significant area of pig farming within Europe and could provide important information on the characterization and circulation of porcine viruses, such as PPIV‐1. With its recent detection in Hungary, these findings suggest widespread circulation of PPIV‐1 in Central Europe, highlighting the need for further research on persistence, pathogenicity and transmission in Europe.
Collapse
Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Erley Lizarazo-Forero
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | | | - Jan Boehmer
- IVD Innovative Veterinary Diagnostics (IVD GmbH), Seelze, Germany
| | - Sabine Schuetze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Sandra Loebert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Juergen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Alex W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| |
Collapse
|
6
|
Kleine Bardenhorst S, Berger T, Klawonn F, Vital M, Karch A, Rübsamen N. Data Analysis Strategies for Microbiome Studies in Human Populations-a Systematic Review of Current Practice. mSystems 2021; 6:e01154-20. [PMID: 33622856 DOI: 10.1128/mSystems.01154-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Reproducibility is a major issue in microbiome studies, which is partly caused by missing consensus about data analysis strategies. The complex nature of microbiome data, which are high-dimensional, zero-inflated, and compositional, makes them challenging to analyze, as they often violate assumptions of classic statistical methods. With advances in human microbiome research, research questions and study designs increase in complexity so that more sophisticated data analysis concepts are applied. To improve current practice of the analysis of microbiome studies, it is important to understand what kind of research questions are asked and which tools are used to answer these questions. We conducted a systematic literature review considering all publications focusing on the analysis of human microbiome data from June 2018 to June 2019. Of 1,444 studies screened, 419 fulfilled the inclusion criteria. Information about research questions, study designs, and analysis strategies were extracted. The results confirmed the expected shift to more advanced research questions, as one-third of the studies analyzed clustered data. Although heterogeneity in the methods used was found at any stage of the analysis process, it was largest for differential abundance testing. Especially if the underlying data structure was clustered, we identified a lack of use of methods that appropriately addressed the underlying data structure while taking into account additional dependencies in the data. Our results confirm considerable heterogeneity in analysis strategies among microbiome studies; increasingly complex research questions require better guidance for analysis strategies. IMPORTANCE The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods. However, the development of suitable analytical methods for analyzing microbiome data has not kept pace with the rapid progression in the field. It is crucial to understand current practice to identify the scope for development. Our results highlight the need for an extensive evaluation of the strengths and shortcomings of existing methods in order to guide the choice of proper analysis strategies. We have identified where new methods could be designed to address more advanced research questions while taking into account the complex structure of the data.
Collapse
|
7
|
Lai WT, Deng WF, Xu SX, Zhao J, Xu D, Liu YH, Guo YY, Wang MB, He FS, Ye SW, Yang QF, Liu TB, Zhang YL, Wang S, Li MZ, Yang YJ, Xie XH, Rong H. Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in major depressive disorder patients. Psychol Med 2021; 51:90-101. [PMID: 31685046 DOI: 10.1017/s0033291719003027] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND The microbiota-gut-brain axis, especially the microbial tryptophan (Trp) biosynthesis and metabolism pathway (MiTBamp), may play a critical role in the pathogenesis of major depressive disorder (MDD). However, studies on the MiTBamp in MDD are lacking. The aim of the present study was to analyze the gut microbiota composition and the MiTBamp in MDD patients. METHODS We performed shotgun metagenomic sequencing of stool samples from 26 MDD patients and 29 healthy controls (HCs). In addition to the microbiota community and the MiTBamp analyses, we also built a classification based on the Random Forests (RF) and Boruta algorithm to identify the gut microbiota as biomarkers for MDD. RESULTS The Bacteroidetes abundance was strongly reduced whereas that of Actinobacteria was significantly increased in the MDD patients compared with the abundance in the HCs. Most noteworthy, the MDD patients had increased levels of Bifidobacterium, which is commonly used as a probiotic. Four Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K01817, K11358, K01626, K01667) abundances in the MiTBamp were significantly lower in the MDD group. Furthermore, we found a negative correlation between the K01626 abundance and the HAMD scores in the MDD group. Finally, RF classification at the genus level can achieve an area under the receiver operating characteristic curve of 0.890. CONCLUSIONS The present findings enabled a better understanding of the changes in gut microbiota and the related Trp pathway in MDD. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing MDD patients form HCs.
Collapse
Affiliation(s)
- Wen-Tao Lai
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Wen-Feng Deng
- Laboratory of Brain Stimulation and Biological Psychiatry, Brain Function and Psychosomatic Medicine Institute, Second People's Hospital of Huizhou, Huizhou, Guangdong, China
| | - Shu-Xian Xu
- Laboratory of Brain Stimulation and Biological Psychiatry, Brain Function and Psychosomatic Medicine Institute, Second People's Hospital of Huizhou, Huizhou, Guangdong, China
| | - Jie Zhao
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Dan Xu
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Yang-Hui Liu
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Yuan-Yuan Guo
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Ming-Bang Wang
- Xiamen Branch, Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | | | - Shu-Wei Ye
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Qi-Fan Yang
- Laboratory of Brain Stimulation and Biological Psychiatry, Brain Function and Psychosomatic Medicine Institute, Second People's Hospital of Huizhou, Huizhou, Guangdong, China
| | - Tie-Bang Liu
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Ying-Li Zhang
- Department of Depression, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Sheng Wang
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Min-Zhi Li
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Ying-Jia Yang
- Department of Depression, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
| | - Xin-Hui Xie
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
- Laboratory of Brain Stimulation and Biological Psychiatry, Brain Function and Psychosomatic Medicine Institute, Second People's Hospital of Huizhou, Huizhou, Guangdong, China
- Center of Acute Psychiatry Service, Second People's Hospital of Huizhou, Huizhou, Guangdong, China
| | - Han Rong
- Department of Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, Guangdong, China
- Affiliated Shenzhen Clinical College of Psychiatry, Jining Medical University, Jining, Shandong, China
| |
Collapse
|
8
|
Sui HY, Weil AA, Nuwagira E, Qadri F, Ryan ET, Mezzari MP, Phipatanakul W, Lai PS. Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing. Front Microbiol 2020; 11:953. [PMID: 32528434 PMCID: PMC7262970 DOI: 10.3389/fmicb.2020.00953] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 02/19/2020] [Accepted: 04/21/2020] [Indexed: 12/26/2022] Open
Abstract
Both the host microbiome and the microbiome of the built environment can have profound impacts on human health. While prior studies have suggested that the variability introduced by DNA extraction method is less than typical biologic variation, most studies have focused on 16S rRNA amplicon sequencing or on high biomass fecal samples. Shotgun metagenomic sequencing provides advantages over amplicon sequencing for surveying the microbiome, but is a challenge to perform in lower microbial biomass samples with high human DNA content such as sputum or vacuumed dust. Here we systematically evaluate the impact of four different extraction methods (phenol:choloroform, and three high-throughput kit-based approaches, the Promega Maxwell gDNA, Qiagen MagAttract PowerSoil DNA, and ZymoBIOMICS 96 MagBead). We report the variation in microbial community structure and predicted microbial function assessed by shotgun metagenomics sequencing in human stool, sputum, and vacuumed dust obtained from ongoing cohort studies or clinical trials. The same beadbeating protocol was used for all samples to focus our evaluation on the impact of kit chemistries on sequencing results. DNA yield was overall highest in the phenol:choloroform and Promega approaches. Only the phenol:choloroform approach showed evidence of contamination in negative controls. Bias was evaluated using mock community controls, and was noted across all extraction methods, although Promega exhibited the least amount of bias. The extraction method did not impact the proportion of human reads, although stool had the lowest proportion of human reads (0.1%) as compared to dust (44.1%) and sputum (80%). We calculated Bray-Curtis dissimilarity and Aitchison distances to evaluate the impact of extraction method on microbial community structure by sample type. Extraction method had the lowest impact in stool (extraction method responsible for 3.0-3.9% of the variability), the most impact in vacuumed dust (12-16% of the variability) and intermediate values for sputum (9.2-12% variability). Similar differences were noted when evaluating microbial community function. Our results will inform investigators planning microbiome studies using diverse sample types in large clinical studies. A consistent DNA extraction approach across all sample types is recommended, particularly with lower microbial biomass samples that are more heavily influenced by extraction method.
Collapse
Affiliation(s)
- Hui-yu Sui
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Ana A. Weil
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States,Harvard Medical School, Boston, MA, United States
| | - Edwin Nuwagira
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States,Harvard Medical School, Boston, MA, United States
| | - Melissa P. Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Wanda Phipatanakul
- Harvard Medical School, Boston, MA, United States,Division of Immunology, Boston Children’s Hospital, Boston, MA, United States
| | - Peggy S. Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States,Harvard Medical School, Boston, MA, United States,Division of Immunology, Boston Children’s Hospital, Boston, MA, United States,*Correspondence: Peggy S. Lai, ;
| |
Collapse
|
9
|
Wan L, Ge WR, Zhang S, Sun YL, Wang B, Yang G. Case-Control Study of the Effects of Gut Microbiota Composition on Neurotransmitter Metabolic Pathways in Children With Attention Deficit Hyperactivity Disorder. Front Neurosci 2020; 14:127. [PMID: 32132899 PMCID: PMC7040164 DOI: 10.3389/fnins.2020.00127] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 10/16/2019] [Accepted: 01/31/2020] [Indexed: 01/08/2023] Open
Abstract
Background Attention-deficit/hyperactivity disorder (ADHD) is a neuropsychiatric condition that may be related to an imbalance of neural transmitters. The gut microbiota is the largest ecosystem in the human body, and the brain-gut axis theory proposes that the gut microbiome can affect brain function in multiple ways. The purpose of this study was to explore the gut microbiota in children with ADHD and assess the possible role of the gut microbiota in disease pathogenesis to open new avenues for ADHD treatment. Methods A case-control design was used. We enrolled 17 children aged 6-12 years with ADHD who were treated in the Pediatric Outpatient Department of the First Medical Center of the Chinese PLA General Hospital from January to June, 2019. Seventeen children aged 6-12 years were selected as the healthy control (HC) group. Fecal samples of cases and controls were analyzed by shotgun metagenomics sequencing. Alpha diversity and the differences in the relative abundances of bacteria were compared between the two groups. Functional annotations were performed for the microbiota genes and metabolic pathways were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG). Results There was no significant difference in the alpha diversity of gut microbiota between the ADHD and HC groups. Compared with HCs, Faecalibacterium and Veillonellaceae were significantly reduced in children with ADHD (P < 0.05), Odoribacter and Enterococcus were significantly increased [linear discriminant analysis (LDA) > 2]. At the species level, Faecalibacterium prausnitzii, Lachnospiraceae bacterium, and Ruminococcus gnavus were significantly reduced in the ADHD group (P < 0.05), while Bacteroides caccae, Odoribacter splanchnicus, Paraprevotella xylaniphila, and Veillonella parvula were increased (P < 0.05). Metabolic pathway analysis revealed significant between-group differences in the metabolic pathways of neurotransmitters (e.g., serotonin and dopamine) (P < 0.05). Conclusion Composition differences of gut microbiota in subjects with ADHD may contribute to brain-gut axis alterations and affect neurotransmitter levels, which could contribute to ADHD symptoms.
Collapse
Affiliation(s)
- Lin Wan
- The First Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Wen-Rong Ge
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Shan Zhang
- The First Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Yu-Lin Sun
- The First Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Bin Wang
- The First Medical Center of the Chinese PLA General Hospital, Beijing, China
| | - Guang Yang
- The First Medical Center of the Chinese PLA General Hospital, Beijing, China
| |
Collapse
|