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Abdill RJ, Graham SP, Rubinetti V, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. bioRxiv 2023:2023.10.11.560955. [PMID: 37873416 PMCID: PMC10592789 DOI: 10.1101/2023.10.11.560955] [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] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Understanding the factors that shape variation in the human microbiome is a major goal of research in biology. While other genomics fields have used large, pre-compiled compendia to extract systematic insights requiring otherwise impractical sample sizes, there has been no comparable resource for the 16S rRNA sequencing data commonly used to quantify microbiome composition. To help close this gap, we have assembled a set of 168,484 publicly available human gut microbiome samples, processed with a single pipeline and combined into the largest unified microbiome dataset to date. We use this resource, which is freely available at microbiomap.org, to shed light on global variation in the human gut microbiome. We find that Firmicutes, particularly Bacilli and Clostridia, are almost universally present in the human gut. At the same time, the relative abundance of the 65 most common microbial genera differ between at least two world regions. We also show that gut microbiomes in undersampled world regions, such as Central and Southern Asia, differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America. Moreover, humans in these overlooked regions likely harbor hundreds of taxa that have not yet been discovered due to this undersampling, highlighting the need for diversity in microbiome studies. We anticipate that this new compendium can serve the community and enable advanced applied and methodological research.
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Affiliation(s)
- Richard J. Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Samantha P. Graham
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vincent Rubinetti
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Sean Davis
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
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Lymberopoulos E, Gentili GI, Alomari M, Sharma N. Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome. Front Artif Intell 2021; 4:680564. [PMID: 34490420 PMCID: PMC8417942 DOI: 10.3389/frai.2021.680564] [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: 03/14/2021] [Accepted: 07/28/2021] [Indexed: 01/22/2023] Open
Abstract
Background: There is growing interest in the connection between the gut microbiome and human health and disease. Conventional approaches to analyse microbiome data typically entail dimensionality reduction and assume linearity of the observed relationships, however, the microbiome is a highly complex ecosystem marked by non-linear relationships. In this study, we use topological data analysis (TDA) to explore differences and similarities between the gut microbiome across several countries. Methods: We used curated adult microbiome data at the genus level from the GMrepo database. The dataset contains OTU and demographical data of over 4,400 samples from 19 studies, spanning 12 countries. We analysed the data with tmap, an integrative framework for TDA specifically designed for stratification and enrichment analysis of population-based gut microbiome datasets. Results: We find associations between specific microbial genera and groups of countries. Specifically, both the USA and UK were significantly co-enriched with the proinflammatory genera Lachnoclostridium and Ruminiclostridium, while France and New Zealand were co-enriched with other, butyrate-producing, taxa of the order Clostridiales. Conclusion: The TDA approach demonstrates the overlap and distinctions of microbiome composition between and within countries. This yields unique insights into complex associations in the dataset, a finding not possible with conventional approaches. It highlights the potential utility of TDA as a complementary tool in microbiome research, particularly for large population-scale datasets, and suggests further analysis on the effects of diet and other regionally varying factors.
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Affiliation(s)
- Eva Lymberopoulos
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom.,CDT AI-Enabled Healthcare Systems, Institute of Health Informatics, University College London, London, United Kingdom
| | - Giorgia Isabella Gentili
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom
| | - Muhannad Alomari
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom.,R Data Labs, Rolls-Royce Ltd, Derby, United Kingdom
| | - Nikhil Sharma
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom.,National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
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Scott GR, Stull KE, Sbei AN, McKinney M, Boling SR, Irish JD. Rocker jaw: Global context for a Polynesian characteristic. Anat Rec (Hoboken) 2020; 304:1776-1791. [PMID: 33159494 DOI: 10.1002/ar.24566] [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: 08/23/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/11/2022]
Abstract
Our goal is to describe the global distribution of the "rocker jaw" variant in human populations. Rocker jaw refers to mandibles that lack the antegonial notch, making them unstable on a flat surface. Data were collected by C.G. Turner II on 9,207 individuals from Asia, Europe, the Pacific, and the Americas, and by J.D. Irish on 3,526 individuals from North and South Africa. With a focus on Polynesia, where the trait is most common, frequencies are presented for subdivisions of Oceania, Australasia, Eurasia, the Americas, and Africa. While the rocker jaw is a Polynesian characteristic, the trait is found throughout the world. Within major geographic regions, there are interesting contrasts, for example, (a) the similarity of Jomon and Ainu and their difference from modern Japanese; (b) Aleuts and Northwest Coast Indians are similar and both are distinct from the Inuit and other Native Americans; and (c) North and Sub-Saharan Africans show a regional difference that parallels genetic and dental distinctions. Skeletons in South America that exhibit the rocker jaw have been interpreted as Polynesian voyagers who ventured to the west coast of South America. The rarity of rocker jaw in South American natives supports this view. The rocker jaw can be attributed to the unique basicranium morphology and large upper facial height of Polynesians, which highlights the integrated growth of a functional module (i.e., mastication) of the craniofacial complex. The unusually high frequency of the trait in Polynesians is a product of both function and founder effect/genetic drift.
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Affiliation(s)
| | - Kyra E Stull
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - Andrea N Sbei
- Department of Anthropology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Mason McKinney
- Department of Anthropology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Scarlett R Boling
- Department of Anthropology, University of Nevada Reno, Reno, Nevada, USA
| | - Joel D Irish
- Research Centre in Evolutionary Anthropology and Palaeoecology, School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
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Sundberg J, Öhman J, Korytowska M, Wallström M, Kjeller G, Andersson M, Horal P, Lindh M, Giglio D, Kovács A, Sand L, Hirsch JM, Magda Araújo Ferracini L, de Souza ACMF, Parlatescu I, Dobre M, Hinescu ME, Braz-Silva PH, Tovaru S, Hasséus B. High-risk human papillomavirus in patients with oral leukoplakia and oral squamous cell carcinoma-A multi-centre study in Sweden, Brazil and Romania. Oral Dis 2020; 27:183-192. [PMID: 32568421 DOI: 10.1111/odi.13510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/15/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Although causal associations between oral leukoplakia (OL), oral squamous cell carcinoma (OSCC) and high-risk human papillomavirus (HR-HPV) have been speculated upon in several reports, conclusive evidence has not been presented. This study investigates whether the number of cases of HR-HPV in OL has increased over time and whether the prevalence of HR-HPV-positive OL differs in various parts of the world. PATIENTS AND METHODS A total of 432 patients with OL from Sweden, Brazil and Romania were analysed. Patients were divided into historical (1992-2002) and contemporary (2011-2017) cohorts from the respective countries. Seventeen patients with OL developed oral squamous cell carcinoma (OSCC). A real-time PCR assay, targeting HPV sub-types 6,11,16,18,31,33,35,39,45,52,56,58 and 59, was performed to detect HR-HPV in patients with OL. RESULTS In the Swedish and Romanian cohorts, none of the investigated HPV sub-types were detected. In the Brazilian cohorts, five patients with OL (3%) were positive for HR-HPV, including four patients from the contemporary cohort (HPV 16, 31, 33) and one from the historical cohort (HPV 11). All the cases of OL that transformed into OSCC were HR-HPV-negative, as were the corresponding tumours. CONCLUSIONS In summary, the prevalence of HR-HPV in OL is low in all the tested countries, and the incidence has not changed over time. HR-HPV in OL does not seem to be a driver of oncogenesis.
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Affiliation(s)
- Jonas Sundberg
- Department of Oral Medicine and Pathology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jenny Öhman
- Department of Oral Medicine and Pathology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magdalena Korytowska
- Clinic of Oral Medicine, Public Dental Service, Region Västra Götaland, NÄL Hospital, Trollhättan, Sweden
| | - Mats Wallström
- Department of Oral and Maxillofacial Surgery, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Göran Kjeller
- Department of Oral and Maxillofacial Surgery, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria Andersson
- Department of Infectious Medicine, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter Horal
- Department of Infectious Medicine, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Medicine, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Giglio
- Department of Oncology, Institute of Clinical Sciences, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lars Sand
- Department of Oral Biology, Faculty of Odontology, University of Oslo, Oslo, Norway
| | - Jan-Michaél Hirsch
- Department of Surgical Sciences, Oral and Maxillofacial Surgery, Uppsala University, Uppsala, Sweden
| | | | | | - Ioanina Parlatescu
- Faculty of Dental Medicine, Oral Pathology Discipline, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Maria Dobre
- Victor Babes Institute of Pathology, Bucharest, Romania
| | - Mihail-Eugen Hinescu
- Faculty of Dental Medicine, Oral Pathology Discipline, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Victor Babes Institute of Pathology, Bucharest, Romania
| | - Paulo Henrique Braz-Silva
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Virology, School of Medicine, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Serban Tovaru
- Faculty of Dental Medicine, Oral Pathology Discipline, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, Institute of Odontology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Clinic of Oral Medicine, Gothenburg, Public Dental Service, Region Västra Götaland, Gothenburg, Sweden
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Abstract
Regional variation in treatment paradigms for gastric adenocarcinoma has attracted a great deal of interest. Between Asia and the West, major differences have been identified in tumor biology, implementation of screening programs, extent of surgical lymphadenectomy, and routine use of neoadjuvant versus adjuvant treatment strategies. Minimally invasive techniques, including both laparoscopic and robotic platforms, have been studied in both regions, with attention to safety, feasibility, and long-term oncologic outcomes. The purpose of this review is to discuss advances in the understanding of the etiology and underlying biology of gastric cancer, as well as the current state of management, focusing on the differences between Asia and the West.
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Affiliation(s)
- Ashley E Russo
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; ,
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; ,
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El Howati A, Tappuni A. Systematic review of the changing pattern of the oral manifestations of HIV. ACTA ACUST UNITED AC 2018; 9:e12351. [PMID: 30019446 DOI: 10.1111/jicd.12351] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 11/27/2022]
Abstract
The purpose of the present study paper was to review the reported prevalence of the oral manifestations of HIV (OM-HIV) worldwide since 1980, and to determine the global variation in its prevalence over time. PubMed, Scopus, Embase and Google Scholar were searched. The filter "English" was used. The timeframe searched was 1980- 2015. The PRISMA flow chart was used. Data were extracted using the Joanna Briggs Institute standardized data extraction form and transferred to SPSS version 22 for analysis. The systematic review of 97 studies (70 low bias risk) showed that the prevalence of OM-HIV continue to be significant in developing countries. Globally and through all the decades, oral candidiasis remained the most commonly encountered OM-HIV, including among patients on antiretroviral therapy (ART) (26.2%). Hairy leukoplakia was more prevalent in Europe and America compared with Africa and Asia. Oral warts were reported more often in studies on patients receiving ART. Interestingly, salivary gland disease decreased in the developed world and increased in developing countries over time. Despite the changing pattern of these conditions over time, there is no evidence that the OM-HIV have become of less significance globally. Maintaining the drive for high-quality research in the subject will have an impact on less developed countries to help address oral health inequalities.
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Affiliation(s)
- Asma El Howati
- Department of Oral Medicine, Institute of Dentistry, Queen Mary University of London, London, UK.,Department of Oral Medicine, Faculty of Dentistry, Benghazi (Garyounis) University, Benghazi, Libya.,Department of Oral Medicine and Oral Surgery, Faculty of Dentistry, Libyan International Medical University, Benghazi, Libya
| | - Anwar Tappuni
- Department of Oral Medicine, Institute of Dentistry, Queen Mary University of London, London, UK
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