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Sun Z, Ning Z, Figeys D. The Landscape and Perspectives of the Human Gut Metaproteomics. Mol Cell Proteomics 2024; 23:100763. [PMID: 38608842 PMCID: PMC11098955 DOI: 10.1016/j.mcpro.2024.100763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
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Affiliation(s)
- Zhongzhi Sun
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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2
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Ahammad I, Bhattacharjee A, Chowdhury ZM, Rahman A, Hossain MU, Dewan G, Talukder S, Das KC, Keya CA, Salimullah M. Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh. Commun Biol 2024; 7:500. [PMID: 38664512 PMCID: PMC11045797 DOI: 10.1038/s42003-024-06191-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, Khyang, and Tripura) residing in the Chittagong Hill Tracts areas of Bangladesh. Following fecal sample collection from each population, part of the bacterial 16 s rRNA gene was amplified and sequenced using Illumina NovaSeq platform. Our findings indicated that Bangladeshi gut microbiota have a distinct diversity profile when compared to other countries. We also found out that Bangladeshi indigenous communities had a higher Firmicutes to Bacteroidetes ratio than the Bengali population. The investigation revealed an unclassified bacterium that was differentially abundant in Bengali samples while the genus Alistipes was found to be prevalent in Chakma samples. Further research on these bacteria might help understand diseases associated with these populations. Also, the current small sample-sized pilot study hindered the comprehensive understanding of the gut microbial diversity of the Bangladeshi population and its potential health implications. However, our study will help establish a basic understanding of the gut microbiome of the Bangladeshi population.
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Affiliation(s)
- Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Zeshan Mahmud Chowdhury
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Anisur Rahman
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Gourab Dewan
- Rangamati Medical College, Hospital Road, Rangamati-4500, Rangamati, Bangladesh
| | - Shiny Talukder
- Rangamati Medical College, Hospital Road, Rangamati-4500, Rangamati, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka, 1229, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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3
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Peeters J, Bot DM, Rovelo Ruiz G, Aerts J. Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs. FRONTIERS IN BIOINFORMATICS 2024; 4:1331043. [PMID: 38375239 PMCID: PMC10875061 DOI: 10.3389/fbinf.2024.1331043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.
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Affiliation(s)
- Jannes Peeters
- Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Daniël M. Bot
- Data Science Institute, Hasselt University, Diepenbeek, Belgium
| | - Gustavo Rovelo Ruiz
- Expertise Center for Digital Media, Hasselt University—Flanders Make, Diepenbeek, Belgium
| | - Jan Aerts
- Visual Data Analysis Lab, Department of Biosystems, KU Leuven, Leuven, Belgium
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4
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Vazquez-Medina A, Rodriguez-Trujillo N, Ayuso-Rodriguez K, Marini-Martinez F, Angeli-Morales R, Caussade-Silvestrini G, Godoy-Vitorino F, Chorna N. Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis. Front Microbiol 2024; 15:1326584. [PMID: 38318337 PMCID: PMC10838991 DOI: 10.3389/fmicb.2024.1326584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
The emergent recognition of the gut-brain axis connection has shed light on the role of the microbiota in modulating the gut-brain axis's functions. Several microbial metabolites, such as serotonin, kynurenine, tryptamine, indole, and their derivatives originating from tryptophan metabolism have been implicated in influencing this axis. In our study, we aimed to investigate the impact of running exercises on microbial tryptophan metabolism using a mouse model. We conducted a multi-omics analysis to obtain a comprehensive insight into the changes in tryptophan metabolism along the microbiota-gut-brain axis induced by running exercises. The analyses integrated multiple components, such as tryptophan changes and metabolite levels in the gut, blood, hippocampus, and brainstem. Fecal microbiota analysis aimed to examine the composition and diversity of the gut microbiota, and taxon-function analysis explored the associations between specific microbial taxa and functional activities in tryptophan metabolism. Our findings revealed significant alterations in tryptophan metabolism across multiple sites, including the gut, blood, hippocampus, and brainstem. The outcomes indicate a shift in microbiota diversity and tryptophan metabolizing capabilities within the running group, linked to increased tryptophan transportation to the hippocampus and brainstem through circulation. Moreover, the symbiotic association between Romboutsia and A. muciniphila indicated their potential contribution to modifying the gut microenvironment and influencing tryptophan transport to the hippocampus and brainstem. These findings have potential applications for developing microbiota-based approaches in the context of exercise for neurological diseases, especially on mental health and overall well-being.
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Affiliation(s)
- Alejandra Vazquez-Medina
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Nicole Rodriguez-Trujillo
- Nutrition and Dietetics Program, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Kiara Ayuso-Rodriguez
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | | | - Roberto Angeli-Morales
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | | | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Nataliya Chorna
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
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5
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Farjana N, Furukawa H, Sumi H, Yumoto I. Effect of Fermentation Scale on Microbiota Dynamics and Metabolic Functions for Indigo Reduction. Int J Mol Sci 2023; 24:14696. [PMID: 37834143 PMCID: PMC10572741 DOI: 10.3390/ijms241914696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
During indigo dyeing fermentation, indigo reduction for the solubilization of indigo particles occurs through the action of microbiota under anaerobic alkaline conditions. The original microbiota in the raw material (sukumo: composted indigo plant) should be appropriately converged toward the extracellular electron transfer (EET)-occurring microbiota by adjusting environmental factors for indigo reduction. The convergence mechanisms of microbiota, microbial physiological basis for indigo reduction, and microbiota led by different velocities in the decrease in redox potential (ORP) at different fermentation scales were analyzed. A rapid ORP decrease was realized in the big batch, excluding Actinomycetota effectively and dominating Alkalibacterium, which largely contributed to the effective indigo reduction. Functional analyses of the microbiota related to strong indigo reduction on approximately day 30 indicated that the carbohydrate metabolism, prokaryotic defense system, and gene regulatory functions are important. Because the major constituent in the big batch was Alkalibacterium pelagium, we attempted to identify genes related to EET in its genome. Each set of genes for flavin adenine dinucleotide (FAD) transportation to modify the flavin mononucleotide (FMN)-associated family, electron transfer from NADH to the FMN-associated family, and demethylmenaquinone (DMK) synthesis were identified in the genome sequence. The correlation between indigo intensity reduction and metabolic functions suggests that V/A-type H+/Na+-transporting ATPase and NAD(P)H-producing enzymes drive membrane transportations and energization in the EET system, respectively.
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Affiliation(s)
- Nowshin Farjana
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiromitsu Furukawa
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan;
| | - Hisako Sumi
- North-Indigo Textile Arts Studio, Otaru 047-0022, Japan;
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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6
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Gomeiz AT, Sun Y, Newborn A, Wang ZW, Angelotti B, Van Aken B. Metagenomic Analysis of a Continuous-Flow Aerobic Granulation System for Wastewater Treatment. Microorganisms 2023; 11:2328. [PMID: 37764172 PMCID: PMC10535324 DOI: 10.3390/microorganisms11092328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Aerobic granulation is an emerging process in wastewater treatment that has the potential to accelerate sedimentation of the microbial biomass during secondary treatment. Aerobic granulation has been difficult to achieve in the continuous flow reactors (CFRs) used in modern wastewater treatment plants. Recent research has demonstrated that the alternation of nutrient-abundant (feast) and nutrient-limiting (famine) conditions is able to promote aerobic granulation in a CFR. In this study, we conducted a metagenomic analysis with the objective of characterizing the bacterial composition of the granular biomass developed in three simulated plug flow reactors (PFRs) with different feast-to-famine ratios. Phylogenetic analyses revealed a clear distinction between the bacterial composition of aerobic granules in the pilot simulated PFRs as compared with conventional activated sludge. Larger and denser granules, showing improved sedimentation properties, were observed in the PFR with the longest famine time and were characterized by a greater proportion of bacteria producing abundant extracellular polymeric substances (EPS). Functional metagenomic analysis based on KEGG pathways indicated that the large and dense aerobic granules in the PFR with the longest famine time showed increased functionalities related to secretion systems and quorum sensing, which are characteristics of bacteria in biofilms and aerobic granules. This study contributes to a further understanding of the relationship between aerobic granule morphology and the bacterial composition of the granular biomass.
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Affiliation(s)
- Alison T. Gomeiz
- School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA;
| | - Yewei Sun
- Hazen and Sawyer, 4035 Ridge Top Road, Fairfax, VA 22030, USA;
| | - Aaron Newborn
- Department of Chemistry and Biochemistry, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Zhi-Wu Wang
- Department of Biological Systems Engineering, Virginia Tech, 1230 Washington St. SW, Blacksburg, VA 24061, USA;
| | - Bob Angelotti
- Upper Occoquan Service Authority, 14631 Compton Rd, Centreville, VA 20121, USA;
| | - Benoit Van Aken
- Department of Chemistry and Biochemistry, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
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7
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Karpe AV, Beale DJ, Tran CD. Intelligent Biological Networks: Improving Anti-Microbial Resistance Resilience through Nutritional Interventions to Understand Protozoal Gut Infections. Microorganisms 2023; 11:1800. [PMID: 37512972 PMCID: PMC10383877 DOI: 10.3390/microorganisms11071800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Enteric protozoan pathogenic infections significantly contribute to the global burden of gastrointestinal illnesses. Their occurrence is considerable within remote and indigenous communities and regions due to reduced access to clean water and adequate sanitation. The robustness of these pathogens leads to a requirement of harsh treatment methods, such as medicinal drugs or antibiotics. However, in addition to protozoal infection itself, these treatments impact the gut microbiome and create dysbiosis. This often leads to opportunistic pathogen invasion, anti-microbial resistance, or functional gastrointestinal disorders, such as irritable bowel syndrome. Moreover, these impacts do not remain confined to the gut and are reflected across the gut-brain, gut-liver, and gut-lung axes, among others. Therefore, apart from medicinal treatment, nutritional supplementation is also a key aspect of providing recovery from this dysbiosis. Future proteins, prebiotics, probiotics, synbiotics, and food formulations offer a good solution to remedy this dysbiosis. Furthermore, nutritional supplementation also helps to build resilience against opportunistic pathogens and potential future infections and disorders that may arise due to the dysbiosis. Systems biology techniques have shown to be highly effective tools to understand the biochemistry of these processes. Systems biology techniques characterize the fundamental host-pathogen interaction biochemical pathways at various infection and recovery stages. This same mechanism also allows the impact of the abovementioned treatment methods of gut microbiome remediation to be tracked. This manuscript discusses system biology approaches, analytical techniques, and interaction and association networks, to understand (1) infection mechanisms and current global status; (2) cross-organ impacts of dysbiosis, particularly within the gut-liver and gut-lung axes; and (3) nutritional interventions. This study highlights the impact of anti-microbial resistance and multi-drug resistance from the perspective of protozoal infections. It also highlights the role of nutritional interventions to add resilience against the chronic problems caused by these phenomena.
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Affiliation(s)
- Avinash V Karpe
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Black Mountain Science and Innovation Park, Acton, ACT 2601, Australia
- Socio-Eternal Thinking for Unity (SETU), Melbourne, VIC 3805, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Cuong D Tran
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Gate 13 Kintore Ave., Adelaide, SA 5000, Australia
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8
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Luiz FN, Passarini MRZ, Magrini FE, Gaio J, Somer JG, Meyer RF, Paesi S. Metataxonomic characterization of the microbial community involved in the production of biogas with microcrystalline cellulose in pilot and laboratory scale. World J Microbiol Biotechnol 2023; 39:184. [PMID: 37147463 DOI: 10.1007/s11274-023-03573-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/08/2023] [Indexed: 05/07/2023]
Abstract
Biogas, produced in anaerobic digestion, is a sustainable alternative for generating energy from agro-industrial and municipal waste. Information from the microbiota active in the process expands the possibilities for technological innovation. In this study, taxonomic annotations, and functional prediction of the microbial community of the inoculum of two processes were carried out: an industrial unit (pilot-scale urban solid waste plant-IU) and a laboratory-scale reactor fed with swine and cattle waste (LS). The biochemical potential of biogas was obtained using tested inoculum with microcrystalline cellulose, obtaining 682 LN/kgVS (LSC-laboratory scale inoculum and microcrystalline cellulose), and 583 LN/kgVS (IUC-industrial unit inoculum and microcrystalline cellulose), which is equivalent to a recovery of 91.5% of total biogas to LSC. The phyla Synergistota and Firmicutes were more abundant in LS/LSC. In the IU/IUC (treatment of restaurant waste and customs seizures), there was a greater microbiological variety and a predominance of the Bacteroidota, Cloacimonadota, Firmicutes and Caldatribacteriota. The genus Methanosaeta predominated in the process, and it was possible to infer the genes (K01895, K00193 and K00625) related to acetoclastic pathway, as well as endoglucanases that are involved in the metabolism of cellulose (LSC). Terpenoids, polyketides, cofactors, and vitamin metabolism were higher in reactors that received different substrates (IU; IUC). The taxonomic and functional differences revealed the importance of determining the microbiota in the analysis of the potential of an inoculum, combined with the use of microcrystalline cellulose, which can provide optimization information in the production of clean energy.
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Affiliation(s)
- Franciele Natividade Luiz
- International Center of Renewable Energy (CIBIOGAS-ER)-Itaipu, Foz do Iguaçu, PR, Brazil
- Federal University of Latin American Integration (UNILA)-Environmental Biotechnology Laboratory, Foz do Iguaçu, PR, Brazil
| | | | - Flaviane Eva Magrini
- Molecular Diagnostic Laboratory, Biotechnology Institute, University of Caxias Do Sul (UCS), Caxias do Sul, RS, 95070-560, Brazil
| | - Juliano Gaio
- Molecular Diagnostic Laboratory, Biotechnology Institute, University of Caxias Do Sul (UCS), Caxias do Sul, RS, 95070-560, Brazil
| | - Juliana Gaio Somer
- International Center of Renewable Energy (CIBIOGAS-ER)-Itaipu, Foz do Iguaçu, PR, Brazil
- Federal University of Latin American Integration (UNILA)-Environmental Biotechnology Laboratory, Foz do Iguaçu, PR, Brazil
| | - Rafaela Faust Meyer
- International Center of Renewable Energy (CIBIOGAS-ER)-Itaipu, Foz do Iguaçu, PR, Brazil
- Federal University of Latin American Integration (UNILA)-Environmental Biotechnology Laboratory, Foz do Iguaçu, PR, Brazil
| | - Suelen Paesi
- Molecular Diagnostic Laboratory, Biotechnology Institute, University of Caxias Do Sul (UCS), Caxias do Sul, RS, 95070-560, Brazil.
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10
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Medriano CA, Chan A, De Sotto R, Bae S. Different types of land use influence soil physiochemical properties, the abundance of nitrifying bacteria, and microbial interactions in tropical urban soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161722. [PMID: 36690092 DOI: 10.1016/j.scitotenv.2023.161722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 107 copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 105 copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27-34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrients and heavy metals and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.
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Affiliation(s)
- Carl Angelo Medriano
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Amabel Chan
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Ryan De Sotto
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Sungwoo Bae
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore.
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11
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Lubin JB, Green J, Maddux S, Denu L, Duranova T, Lanza M, Wynosky-Dolfi M, Flores JN, Grimes LP, Brodsky IE, Planet PJ, Silverman MA. Arresting microbiome development limits immune system maturation and resistance to infection in mice. Cell Host Microbe 2023; 31:554-570.e7. [PMID: 36996818 PMCID: PMC10935632 DOI: 10.1016/j.chom.2023.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/09/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023]
Abstract
Disruptions to the intestinal microbiome during weaning lead to negative effects on host immune function. However, the critical host-microbe interactions during weaning that are required for immune system development remain poorly understood. We find that restricting microbiome maturation during weaning stunts immune system development and increases susceptibility to enteric infection. We developed a gnotobiotic mouse model of the early-life microbiome Pediatric Community (PedsCom). These mice develop fewer peripheral regulatory T cells and less IgA, hallmarks of microbiota-driven immune system development. Furthermore, adult PedsCom mice retain high susceptibility to Salmonella infection, which is characteristic of young mice and children. Altogether, our work illustrates how the post-weaning transition in microbiome composition contributes to normal immune maturation and protection from infection. Accurate modeling of the pre-weaning microbiome provides a window into the microbial requirements for healthy development and suggests an opportunity to design microbial interventions at weaning to improve immune development in human infants.
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Affiliation(s)
- Jean-Bernard Lubin
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jamal Green
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah Maddux
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lidiya Denu
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Tereza Duranova
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew Lanza
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | | | - Julia N Flores
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Logan P Grimes
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, IFI, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Michael A Silverman
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perlman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Immunology Research Unit, GlaxoSmithKline, Collegeville, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Lee CY, Dillard LR, Papin JA, Arnold KB. New perspectives into the vaginal microbiome with systems biology. Trends Microbiol 2023; 31:356-368. [PMID: 36272885 DOI: 10.1016/j.tim.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 10/28/2022]
Abstract
The vaginal microbiome (VMB) is critical to female reproductive health; however, the mechanisms associated with optimal and non-optimal states remain poorly understood due to the complex community structure and dynamic nature. Quantitative systems biology techniques applied to the VMB have improved understanding of community composition and function using primarily statistical methods. In contrast, fewer mechanistic models that use a priori knowledge of VMB features to develop predictive models have been implemented despite their use for microbiomes at other sites, including the gastrointestinal tract. Here, we explore systems biology approaches that have been applied in the VMB, highlighting successful techniques and discussing new directions that hold promise for improving understanding of health and disease.
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Affiliation(s)
- Christina Y Lee
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Lillian R Dillard
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Kelly B Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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13
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García-Amado MA, Rudolf CA, Fuentes-Fuentes MDM, Chorna N, Martínez LM, Godoy-Vitorino F. Bacterial composition along the digestive tract of the Horned Screamer ( Anhima cornuta), a tropical herbivorous bird. PeerJ 2023; 11:e14805. [PMID: 36815987 PMCID: PMC9933741 DOI: 10.7717/peerj.14805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/05/2023] [Indexed: 02/15/2023] Open
Abstract
Background The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela. Methods Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO. Results The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences. Conclusion Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.
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Affiliation(s)
- María Alexandra García-Amado
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Miranda, Venezuela
| | - Carla A. Rudolf
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Miranda, Venezuela
| | | | - Nataliya Chorna
- Biochemistry Department, University of Puerto Rico School of Medicine, San Juan, PR, Puerto Rico
| | | | - Filipa Godoy-Vitorino
- Microbiology Department, University of Puerto Rico, School of Medicine, San Juan, Puerto Rico
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14
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Karpe AV, Hutton ML, Mileto SJ, James ML, Evans C, Ghodke AB, Shah RM, Metcalfe SS, Liu JW, Walsh T, Lyras D, Palombo EA, Beale DJ. Gut Microbial Perturbation and Host Response Induce Redox Pathway Upregulation along the Gut-Liver Axis during Giardiasis in C57BL/6J Mouse Model. Int J Mol Sci 2023; 24:ijms24021636. [PMID: 36675151 PMCID: PMC9862352 DOI: 10.3390/ijms24021636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Apicomplexan infections, such as giardiasis and cryptosporidiosis, negatively impact a considerable proportion of human and commercial livestock populations. Despite this, the molecular mechanisms of disease, particularly the effect on the body beyond the gastrointestinal tract, are still poorly understood. To highlight host-parasite-microbiome biochemical interactions, we utilised integrated metabolomics-16S rRNA genomics and metabolomics-proteomics approaches in a C57BL/6J mouse model of giardiasis and compared these to Cryptosporidium and uropathogenic Escherichia coli (UPEC) infections. Comprehensive samples (faeces, blood, liver, and luminal contents from duodenum, jejunum, ileum, caecum and colon) were collected 10 days post infection and subjected to proteome and metabolome analysis by liquid and gas chromatography-mass spectrometry, respectively. Microbial populations in faeces and luminal washes were examined using 16S rRNA metagenomics. Proteome-metabolome analyses indicated that 12 and 16 key pathways were significantly altered in the gut and liver, respectively, during giardiasis with respect to other infections. Energy pathways including glycolysis and supporting pathways of glyoxylate and dicarboxylate metabolism, and the redox pathway of glutathione metabolism, were upregulated in small intestinal luminal contents and the liver during giardiasis. Metabolomics-16S rRNA genetics integration indicated that populations of three bacterial families-Autopobiaceae (Up), Desulfovibrionaceae (Up), and Akkermanasiaceae (Down)-were most significantly affected across the gut during giardiasis, causing upregulated glycolysis and short-chained fatty acid (SCFA) metabolism. In particular, the perturbed Akkermanasiaceae population seemed to cause oxidative stress responses along the gut-liver axis. Overall, the systems biology approach applied in this study highlighted that the effects of host-parasite-microbiome biochemical interactions extended beyond the gut ecosystem to the gut-liver axis. These findings form the first steps in a comprehensive comparison to ascertain the major molecular and biochemical contributors of host-parasite interactions and contribute towards the development of biomarker discovery and precision health solutions for apicomplexan infections.
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Affiliation(s)
- Avinash V. Karpe
- Environment, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Melanie L. Hutton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3168, Australia
| | - Steven J. Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3168, Australia
| | - Meagan L. James
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3168, Australia
| | - Chris Evans
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3168, Australia
| | - Amol B. Ghodke
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
- Department of Horticulture, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Rohan M. Shah
- Environment, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Suzanne S. Metcalfe
- Environment, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Jian-Wei Liu
- Environment, Commonwealth Scientific and Industrial Research Organization, Agricultural and Environmental Sciences Precinct, Acton, Canberra, ACT 2601, Australia
| | - Tom Walsh
- Environment, Commonwealth Scientific and Industrial Research Organization, Agricultural and Environmental Sciences Precinct, Acton, Canberra, ACT 2601, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3168, Australia
| | - Enzo A. Palombo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - David J. Beale
- Environment, Commonwealth Scientific and Industrial Research Organization, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
- Correspondence:
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15
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Gaio J, Lora NL, Iltchenco J, Magrini FE, Paesi S. Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil. Bioprocess Biosyst Eng 2023; 46:69-87. [PMID: 36401655 DOI: 10.1007/s00449-022-02814-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022]
Abstract
Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.
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Affiliation(s)
- Juliano Gaio
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil.
| | - Naline Laura Lora
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
| | - Janaína Iltchenco
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
| | - Flaviane Eva Magrini
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
| | - Suelen Paesi
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
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16
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Farjana N, Tu Z, Furukawa H, Yumoto I. Environmental factors contributing to the convergence of bacterial community structure during indigo reduction. Front Microbiol 2023; 14:1097595. [PMID: 36876097 PMCID: PMC9978934 DOI: 10.3389/fmicb.2023.1097595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023] Open
Abstract
Indigo is solubilized through the reducing action of the microbiota that occurs during alkaline fermentation of composted leaves of Polygonum tinctorium L. (sukumo). However, the environmental effects on the microbiota during this treatment, as well as the mechanisms underlying the microbial succession toward stable state remain unknown. In this study, physicochemical analyses and Illumina metagenomic sequencing was used to determine the impact pretreatment conditions on the subsequent initiation of bacterial community transition and their convergence, dyeing capacity and the environmental factors critical for indigo reducing state during aging of sukumo. The initial pretreatment conditions analyzed included 60°C tap water (heat treatment: batch 1), 25°C tap water (control; batch 2), 25°C wood ash extract (high pH; batch 3) and hot wood ash extract (heat and high pH; batch 4), coupled with successive addition of wheat bran from days 5 to 194. High pH had larger impact than heat treatment on the microbiota, producing more rapid transitional changes from days 1 to 2. Although the initial bacterial community composition and dyeing intensity differed during days 2-5, the microbiota appropriately converged to facilitate indigo reduction from day 7 in all the batches, with Alkaliphilus oremalandii, Amphibacillus, Alkalicella caledoniensis, Atopostipes suicloalis and Tissierellaceae core taxa contributing to the improvement of when the dyeing intensity. This convergence is attributed to the continuous maintenance of high pH (day 1 ~) and low redox potential (day 2~), along with the introduction of wheat bran at day 5 (day 5~). PICRUSt2 predictive function profiling revealed the enrichment of phosphotransferease system (PTS) and starch and sucrose metabolism subpathways key toward indigo reduction. Seven NAD(P)-dependent oxidoreductases KEGG orthologs correlating to the dyeing intensity was also identified, with Alkalihalobacillus macyae, Alkalicella caledoniensis, and Atopostipes suicloalis contributing significantly toward the initiation of indigo reduction in batch 3. During the ripening period, the staining intensity was maintained by continuous addition of wheat bran and the successive emergence of indigo-reducing bacteria that also contributed to material circulation in the system. The above results provide insight into the interaction of microbial system and environmental factors in sukumo fermentation.
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Affiliation(s)
- Nowshin Farjana
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hiromitsu Furukawa
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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17
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Piro VC, Renard BY. Contamination detection and microbiome exploration with GRIMER. Gigascience 2022; 12:giad017. [PMID: 36994872 PMCID: PMC10061425 DOI: 10.1093/gigascience/giad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Contamination detection is a important step that should be carefully considered in early stages when designing and performing microbiome studies to avoid biased outcomes. Detecting and removing true contaminants is challenging, especially in low-biomass samples or in studies lacking proper controls. Interactive visualizations and analysis platforms are crucial to better guide this step, to help to identify and detect noisy patterns that could potentially be contamination. Additionally, external evidence, like aggregation of several contamination detection methods and the use of common contaminants reported in the literature, could help to discover and mitigate contamination. RESULTS We propose GRIMER, a tool that performs automated analyses and generates a portable and interactive dashboard integrating annotation, taxonomy, and metadata. It unifies several sources of evidence to help detect contamination. GRIMER is independent of quantification methods and directly analyzes contingency tables to create an interactive and offline report. Reports can be created in seconds and are accessible for nonspecialists, providing an intuitive set of charts to explore data distribution among observations and samples and its connections with external sources. Further, we compiled and used an extensive list of possible external contaminant taxa and common contaminants with 210 genera and 627 species reported in 22 published articles. CONCLUSION GRIMER enables visual data exploration and analysis, supporting contamination detection in microbiome studies. The tool and data presented are open source and available at https://gitlab.com/dacs-hpi/grimer.
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Affiliation(s)
- Vitor C Piro
- Data Analytics and Computational Statistics, Hasso Plattner Insititute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - Bernhard Y Renard
- Data Analytics and Computational Statistics, Hasso Plattner Insititute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
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18
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Lopes HDFS, Tu Z, Sumi H, Yumoto I. Indigofera tinctoria L. leaf powder promotes initiation of indigo reduction by inducing of rapid transition of the microbial community. Front Microbiol 2022; 13:957809. [PMID: 36016790 PMCID: PMC9395713 DOI: 10.3389/fmicb.2022.957809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Water-insoluble indigo is solubilized by the reducing action of microorganisms which occurs during fermentation. In natural indigo fermentation, composted leaves of Polygonum tinctorium L. (sukumo) are the raw material that has been used as both the indigo source and the bacterial inoculum. Ideally, indigo reduction occurs shortly after preparation of the fermentation vat. The time-to-reduction depends on the quality of the sukumo and the methods for preparation and management of the fermentation batch. We estimated the effect of adding Indigofera tinctoria L. leaf powder (LP) to indigo fermentation in two fermentations originally exhibiting either rapid or slow time-to-reduction (T-sukumo and D-sukumo, respectively). Alkalihalobacillus spp. (97.7%–98.4% similarities with Alkalihalobacillus macyae) were observed only in the LP-added T-sukumo fermentation liquor. They appeared from day 1 (0.7%) and increased to 24.4% on day 6, and their presence was related to indigo reduction. Differences in functional ratio between LP-added and its control batches revealed enhancement of pathways related to reconstitution of cellular functions and substrate metabolisms, to all of which Alkalihalobacillus spp. contributed intensively. In D-sukumo batch, appearance of bacteria necessary to initiate indigo reduction (principally Anaerobacillus/Polygonibacillus) was comparatively slower. LP promotes earlier indigo reduction in both T- and D-sukumo-based batches, owing to its promotion of microbiota transition. The effect of the LP was intensified from day 1 to day 2 in both sukumo using batches according to the assumed function of the microbiota. The initial effect of LP on the T-sukumo batches was more intense than that in the D-sukumo batches and was continued until day 3, while the duration in the T-sukumo batches was continued until day 5. Based on these observations, we propose that the LP functions through its phytochemicals that eliminate oxygen, stimulate the microbiota, and accelerate its transitional changes toward a suitable function that opens the pathway for the extracellular electron transfer using carbohydrates as a substrate.
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Affiliation(s)
- Helena de Fátima Silva Lopes
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hisako Sumi
- North-Indigo Textile Arts Studio, Otaru, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- *Correspondence: Isao Yumoto,
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19
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Hou J, Song Y, Leung ASY, Tang MF, Shi M, Wang EY, Tsun JGS, Chan RWY, Wong GWK, Tsui SKW, Leung TF. Temporal Dynamics of the Nasopharyngeal Microbiome and its Relationship with Childhood Asthma Exacerbation. Microbiol Spectr 2022; 10:e0012922. [PMID: 35546575 PMCID: PMC9241764 DOI: 10.1128/spectrum.00129-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Despite distinct nasopharyngeal microbiome (NPM) profiles between asthmatics and healthy subjects, little is known about the NPM dynamics and its relation to childhood asthma exacerbation (AE). We investigated NPM changes by longitudinally collecting 135 flocked nasopharyngeal swabs (FNPSs) from 33 school-age asthmatic children at six time points (2 to 4-week intervals) from September to December 2017 in Hong Kong. Subjects were categorized into AE and stable asthma (AS) groups according to whether they experienced any exacerbation during follow-up. One-off FNPSs from nine nonasthmatic children were included as controls. Microbiota profiles were analyzed using 16S rRNA gene sequencing. All 144 NPMs were classified into six microbiome profile groups (MPGs), each dominated by Moraxella, Corynebacterium 1, Dolosigranulum, Staphylococcus, Streptococcus, or Anoxybacillus. The microbial diversity and compositions of NPM in exacerbation samples were different from both baseline samples and those from healthy controls. Moraxella and Dolosigranulum-dominated NPM exhibited high temporal stability revealed by MPG transition analysis. NPM diversity decreased whereas microbial composition remained similar over time. The relative abundances of Moraxella increased while Corynebacterium 1, Anoxybacillus, and Pseudomonas decreased longitudinally. However, these temporal patterns did not differ between AE and AS groups, suggesting that short-term dynamic patterns were not sufficient to predict AE occurrence. Asthmatic NPM underwent Moraxella expansion during AE and presented a high microbiome resilience (recovery potential) after AE resolution. Microbial pathways involved in methane, ketone bodies, and vitamin B3 metabolisms were enhanced during AE and primarily contributed by Moraxella. IMPORTANCE Evidence on the dynamic changes of NPM in asthmatic patients remains limited. Here, we present that asthmatic NPMs deviating from a healthy status still showed resilience after disturbance. Our data imply from a longitudinal perspective that Moraxella increase is closely related to AE occurrence. The finding of functional dysbiosis (imbalance) during AE offers a plausible explanation for the known association between nasopharyngeal Moraxella expansion and increased AE risk. This work serves as a basis for future long-term prospective studies leveraging multiomics approaches to elucidate the temporal association between NPM and pediatric AE.
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Affiliation(s)
- Jinpao Hou
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuping Song
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Agnes Sze Yin Leung
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Man Fung Tang
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Evy Yiwei Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Gar Shun Tsun
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Renee Wan Yi Chan
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
- Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
| | - Gary Wing Kin Wong
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Bioinformatics Center, The Chinese University of Hong Kong, Hong Kong, China
- Center for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fan Leung
- Department of Pediatrics, The Chinese University of Hong Kong, Hong Kong, China
- Department of Pediatrics, Prince of Wales Hospital, Hong Kong, China
- Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
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20
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Parodi G, Leite G, Pimentel ML, Barlow GM, Fiorentino A, Morales W, Pimentel M, Weitsman S, Mathur R. The Response of the Rodent Gut Microbiome to Broad-Spectrum Antibiotics Is Different in Males and Females. Front Microbiol 2022; 13:897283. [PMID: 35756061 PMCID: PMC9218673 DOI: 10.3389/fmicb.2022.897283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Gut microbiome composition is different in males and females, but sex is rarely considered when prescribing antibiotics, and sex-based differences in gut microbiome recovery following antibiotic treatment are poorly understood. Here, we compared the effects of broad-spectrum antibiotics on both the stool and small bowel microbiomes in male and female rats. Adult male and female Sprague Dawley rats were exposed to a multi-drug antibiotic cocktail for 8 days, or remained unexposed as controls. Following cessation of antibiotics, rats were monitored for an additional 13-day recovery period prior to euthanasia. Baseline stool microbiome composition was similar in males and females. By antibiotic exposure day 8 (AbxD8), exposed male rats exhibited greater loss of stool microbial diversity compared to exposed females, and the relative abundance (RA) of numerous taxa were significantly different in exposed males vs. exposed females. Specifically, RA of phylum Proteobacteria and genera Lactobacillus, Sutterella, Akkermansia, and Serratia were higher in exposed males vs. exposed females, whereas RA of phyla Firmicutes and Actinobacteria and genera Turicibacter and Enterococcus were lower. By 13 days post antibiotics cessation (PAbxD13), the stool RA of these and other taxa remained significantly different from baseline, and also remained significantly different between exposed males and exposed females. RA of phyla Firmicutes and Actinobacteria and genus Enterococcus remained lower in exposed males vs. exposed females, and genus Sutterella remained higher. However, RA of phylum Proteobacteria and genus Akkermansia were now also lower in exposed males vs. females, whereas RA of phylum Bacteroidetes and genus Turicibacter were now higher in exposed males. Further, the small bowel microbiome of exposed rats on PAbxD13 was also significantly different from unexposed controls, with higher RA of Firmicutes, Turicibacter and Parabacteroides in exposed males vs. females, and lower RA of Bacteroidetes, Proteobacteria, Actinobacteria, Oscillospira, Sutterella, and Akkermansia in exposed males vs. females. These findings indicate that broad-spectrum antibiotics have significant and sex-specific effects on gut microbial populations in both stool and the small bowel, and that the recovery of gut microbial populations following exposure to broad-spectrum antibiotics also differs between sexes. These findings may have clinical implications for the way antibiotics are prescribed.
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Affiliation(s)
- Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Gabriela Leite
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Maya L Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Alyson Fiorentino
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States.,Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai, Los Angeles, CA, United States
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai, Los Angeles, CA, United States.,Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai, Los Angeles, CA, United States
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21
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A potential oral microbiome signature associated with coronary artery disease in Tunisia. Biosci Rep 2022; 42:231418. [PMID: 35695679 PMCID: PMC9251586 DOI: 10.1042/bsr20220583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/17/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
The coronary artery disease is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with coronary artery disease (CAD). We performed metagenomic profiling of salivary microbiomes by 16S rRNA next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and 10 healthy individuals without carotid plaques or previous stroke or myocardial infarction.We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Rothia), Bacteroidetes (genus Prevotella, Porphyromonas) and Fusobacteria (genus Fusobacterium, Leptotrichia). More than 60% relative abundance of each sample for both CAD patients and controls is represented by three major genera including Streptococcus (24.97% and 26.33%), Veillonella (21.43% and 19.91%) and Neisseria (14.23% and 15.33%). Using penalized regression analysis, the bacterial genus Eikenella was involved as the major discriminant genus for both status and Syntax score of CAD. We also reported a significant negative correlation between Syntax score and Eikenella abundance in coronary patients' group (Spearman rho =-0.68, p= 0.00094). In conclusion, the abundance of Eikenella in oral coronary patient samples compared to controls could be a prominent pathological indicator for the development of CAD.
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22
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Secombe KR, Ball IA, Wignall AD, Bateman E, Keefe DM, Bowen JM. Antibiotic treatment targeting gram negative bacteria prevents neratinib-induced diarrhea in rats. Neoplasia 2022; 30:100806. [PMID: 35561424 PMCID: PMC9111977 DOI: 10.1016/j.neo.2022.100806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/05/2022] [Accepted: 04/28/2022] [Indexed: 12/11/2022]
Abstract
Background Neratinib is a pan-ErbB tyrosine kinase inhibitor used for extended adjuvant treatment of HER2-positive breast cancer. Diarrhea is the main adverse event associated with neratinib treatment. We aimed here to determine whether antibiotic-induced gut microbial shifts altered development of neratinib-induced diarrhea. Methods Female Albino Wistar rats (total n = 44) were given antibiotics (vancomycin, neomycin, or a cocktail of vancomycin, neomycin and ampicillin) in drinking water for four weeks, and then treated daily with neratinib (50 mg/kg) for 28 days. Diarrhea, along with markers of gastrointestinal damage and microbial alterations were measured by histopathology and 16S sequencing, respectively. Results Rats treated with vancomycin or neomycin had significantly lower levels of diarrhea than rats treated with neratinib alone. In the distal ileum, neratinib was associated with a statistically significant increase in histological damage in all treatment groups expect the antibiotic cocktail. Key features included villous blunting and fusion and some inflammatory infiltrate. Differences in microbial composition at necropsy in vehicle control, neratinib and neratinib + neomycin groups, were characterized by a neratinib-induced increase in gram-negative bacteria that was reversed by neomycin. Neomycin shifted bacterial composition so that Blautia become the dominant genus. Conclusions Narrow spectrum antibiotics reduced neratinib-induced diarrhea. This suggests that the microbiome may play a key role in the development and prolongation of diarrhea following neratinib treatment, although further research is required to understand the key bacteria and mechanisms by which they reduce diarrhea, as well as how this may impact presentation of diarrhea in clinical cohorts.
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Affiliation(s)
- Kate R Secombe
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia.
| | - Imogen A Ball
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Anthony D Wignall
- Division of Health Sciences, University of South Australia, South Australia, Australia
| | - Emma Bateman
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Dorothy M Keefe
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Joanne M Bowen
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
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23
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Fortuin S, Soares NC. The Integration of Proteomics and Metabolomics Data Paving the Way for a Better Understanding of the Mechanisms Underlying Microbial Acquired Drug Resistance. Front Med (Lausanne) 2022; 9:849838. [PMID: 35602483 PMCID: PMC9120609 DOI: 10.3389/fmed.2022.849838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Due to an increase in the overuse of antimicrobials and accelerated incidence of drug resistant pathogens, antimicrobial resistance has become a global health threat. In particular, bacterial antimicrobial resistance, in both hospital and community acquired transmission, have been found to be the leading cause of death due to infectious diseases. Understanding the mechanisms of bacterial drug resistance is of clinical significance irrespective of hospital or community acquired since it plays an important role in the treatment strategy and controlling infectious diseases. Here we highlight the advances in mass spectrometry-based proteomics impact in bacterial proteomics and metabolomics analysis- focus on bacterial drug resistance. Advances in omics technologies over the last few decades now allows multi-omics studies in order to obtain a comprehensive understanding of the biochemical alterations of pathogenic bacteria in the context of antibiotic exposure, identify novel biomarkers to develop new drug targets, develop time-effectively screen for drug susceptibility or resistance using proteomics and metabolomics.
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Affiliation(s)
- Suereta Fortuin
- African Microbiome Institute, General Internal Medicine, Stellenbosch University, Cape Town, South Africa
- *Correspondence: Suereta Fortuin
| | - Nelson C. Soares
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Nelson C. Soares
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24
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The gut microbiome of exudivorous marmosets in the wild and captivity. Sci Rep 2022; 12:5049. [PMID: 35322053 PMCID: PMC8942988 DOI: 10.1038/s41598-022-08797-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022] Open
Abstract
Mammalian captive dietary specialists like folivores are prone to gastrointestinal distress and primate dietary specialists suffer the greatest gut microbiome diversity losses in captivity compared to the wild. Marmosets represent another group of dietary specialists, exudivores that eat plant exudates, but whose microbiome remains relatively less studied. The common occurrence of gastrointestinal distress in captive marmosets prompted us to study the Callithrix gut microbiome composition and predictive function through bacterial 16S ribosomal RNA V4 region sequencing. We sampled 59 wild and captive Callithrix across four species and their hybrids. Host environment had a stronger effect on the gut microbiome than host taxon. Wild Callithrix gut microbiomes were enriched for Bifidobacterium, which process host-indigestible carbohydrates. Captive marmoset guts were enriched for Enterobacteriaceae, a family containing pathogenic bacteria. While gut microbiome function was similar across marmosets, Enterobacteriaceae seem to carry out most functional activities in captive host guts. More diverse bacterial taxa seem to perform gut functions in wild marmosets, with Bifidobacterium being important for carbohydrate metabolism. Captive marmosets showed gut microbiome composition aspects seen in human gastrointestinal diseases. Thus, captivity may perturb the exudivore gut microbiome, which raises implications for captive exudivore welfare and calls for husbandry modifications.
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25
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Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022; 20:143-160. [PMID: 34552265 PMCID: PMC9578303 DOI: 10.1038/s41579-021-00621-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Affiliation(s)
- Anelize Bauermeister
- Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Helena Mannochio-Russo
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | | | - Alan K. Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
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26
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Peeters J, Thas O, Shkedy Z, Kodalci L, Musisi C, Owokotomo OE, Dyczko A, Hamad I, Vangronsveld J, Kleinewietfeld M, Thijs S, Aerts J. Exploring the Microbiome Analysis and Visualization Landscape. FRONTIERS IN BIOINFORMATICS 2021; 1:774631. [PMID: 36303773 PMCID: PMC9580862 DOI: 10.3389/fbinf.2021.774631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/29/2021] [Indexed: 02/02/2023] Open
Abstract
Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.
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Affiliation(s)
- Jannes Peeters
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
- *Correspondence: Jannes Peeters ,
| | - Olivier Thas
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | - Ziv Shkedy
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | - Leyla Kodalci
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | - Connie Musisi
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
| | | | - Aleksandra Dyczko
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Diepenbeek, Belgium
- Department of Immunology and Infection, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Ibrahim Hamad
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Diepenbeek, Belgium
- Department of Immunology and Infection, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Faculty of Biology and Biotechnology, Maria Curie–Skłodowska University, Lublin, Poland
| | - Markus Kleinewietfeld
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Diepenbeek, Belgium
- Department of Immunology and Infection, Biomedical Research Institute (BIOMED), Hasselt University, Diepenbeek, Belgium
| | - Sofie Thijs
- Center for Environmental Sciences, Environmental Biology, Hasselt University, Diepenbeek, Belgium
| | - Jan Aerts
- CENSTAT, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium
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27
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Secombe KR, Crame EE, Tam JSY, Wardill HR, Gibson RJ, Coller JK, Bowen JM. Intestinal toll-like receptor 4 knockout alters the functional capacity of the gut microbiome following irinotecan treatment. Cancer Chemother Pharmacol 2021; 89:275-281. [PMID: 34854953 DOI: 10.1007/s00280-021-04382-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/22/2021] [Indexed: 11/27/2022]
Abstract
PURPOSE Irinotecan can cause high levels of diarrhea caused by toxic injury to the gastrointestinal microenvironment. Toll-like receptor 4 (TLR4) and the gut microbiome have previously been implicated in gastrointestinal toxicity and diarrhea; however, the link between these two factors has not been definitively determined. We used a tumor-bearing, intestinal epithelial cell (IEC) TLR4 knockout model (Tlr4ΔIEC) to assess microbiome changes following irinotecan treatment. We then determined if a fecal microbiota transplant (FMT) between Tlr4ΔIEC and wild-type (WT) mice altered irinotecan-induced gastrointestinal toxicity. METHODS MC-38 colorectal cancer cells were injected into WT and Tlr4ΔIEC mice. Fecal samples were collected prior to tumor inoculation, prior to irinotecan treatment and at cull. 16S rRNA gene sequencing was used to assess changes in the microbiome. Next, FMT was used to transfer the microbiome phenotype between Tlr4ΔIEC and WT mice prior to irinotecan treatment. Gastrointestinal toxicity symptoms were assessed. RESULTS In study 1, there were no compositional differences in the microbiome between Tlr4ΔIEC and WT mice at baseline. However, predicted functional capacity of the microbiome was different between WT and Tlr4ΔIEC at baseline and post-irinotecan. In study 2, Tlr4ΔIEC mice were protected from grade 3 diarrhea. Additionally, WT mice who did not receive FMT had more colonic damage in the colon compared to controls (P = 0.013). This was not seen in Tlr4ΔIEC mice or WT mice who received FMT (P > 0.05). CONCLUSION Tlr4ΔIEC and WT had no baseline compositional microbiome differences, but functional differences at baseline and following irinotecan. FMT altered some aspects of irinotecan-induced gastrointestinal toxicity.
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Affiliation(s)
- Kate R Secombe
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia.
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia.
| | - Elise E Crame
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Janine S Y Tam
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Hannah R Wardill
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
- Precision Medicine Theme (Cancer), The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Rachel J Gibson
- School of Allied Health and Practice, University of Adelaide, Adelaide, South Australia, Australia
| | - Janet K Coller
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Joanne M Bowen
- School of Biomedicine, University of Adelaide, Adelaide, South Australia, Australia
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28
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Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021; 22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
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29
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Shah RM, Hillyer KE, Stephenson S, Crosswell J, Karpe AV, Palombo EA, Jones OAH, Gorman D, Bodrossy L, van de Kamp J, Bissett A, Whiteley AS, Steven ADL, Beale DJ. Functional analysis of pristine estuarine marine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146526. [PMID: 33798899 DOI: 10.1016/j.scitotenv.2021.146526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.
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Affiliation(s)
- Rohan M Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia; Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Sarah Stephenson
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, NSW 2234, Australia
| | - Joseph Crosswell
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Avinash V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, Bundoora West Campus, PO Box 71, Bundoora, VIC 3083, Australia
| | - Daniel Gorman
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Indian Ocean Marine Research Centre, Crawley, WA 6009, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew S Whiteley
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA 6014, Australia
| | - Andy D L Steven
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia.
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30
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Granato DC, Neves LX, Trino LD, Carnielli CM, Lopes AFB, Yokoo S, Pauletti BA, Domingues RR, Sá JO, Persinoti G, Paixão DAA, Rivera C, de Sá Patroni FM, Tommazetto G, Santos-Silva AR, Lopes MA, de Castro G, Brandão TB, Prado-Ribeiro AC, Squina FM, Telles GP, Paes Leme AF. Meta-omics analysis indicates the saliva microbiome and its proteins associated with the prognosis of oral cancer patients. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140659. [PMID: 33839314 DOI: 10.1016/j.bbapap.2021.140659] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022]
Abstract
Saliva is a biofluid that maintains the health of oral tissues and the homeostasis of oral microbiota. Studies have demonstrated that Oral squamous cell carcinoma (OSCC) patients have different salivary microbiota than healthy individuals. However, the relationship between these microbial differences and clinicopathological outcomes is still far from conclusive. Herein, we investigate the capability of using metagenomic and metaproteomic saliva profiles to distinguish between Control (C), OSCC without active lesion (L0), and OSCC with active lesion (L1) patients. The results show that there are significantly distinct taxonomies and functional changes in L1 patients compared to C and L0 patients, suggesting compositional modulation of the oral microbiome, as the relative abundances of Centipeda, Veillonella, and Gemella suggested by metagenomics are correlated with tumor size, clinical stage, and active lesion. Metagenomics results also demonstrated that poor overall patient survival is associated with a higher relative abundance of Stenophotromonas, Staphylococcus, Centipeda, Selenomonas, Alloscordovia, and Acitenobacter. Finally, compositional and functional differences in the saliva content by metaproteomics analysis can distinguish healthy individuals from OSCC patients. In summary, our study suggests that oral microbiota and their protein abundance have potential diagnosis and prognosis value for oral cancer patients. Further studies are necessary to understand the role of uniquely detected metaproteins in the microbiota of healthy and OSCC patients as well as the crosstalk between saliva host proteins and the oral microbiome present in OSCC.
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Affiliation(s)
- Daniela C Granato
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Leandro X Neves
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Luciana D Trino
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | | | - Ariane F B Lopes
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Sami Yokoo
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Bianca A Pauletti
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Romênia R Domingues
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Jamile O Sá
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Gabriella Persinoti
- Laboratório Nacional de Biorrenováveis, LNBr, CNPEM, Campinas, São Paulo, Brazil
| | - Douglas A A Paixão
- Laboratório Nacional de Biorrenováveis, LNBr, CNPEM, Campinas, São Paulo, Brazil
| | - César Rivera
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil
| | - Fabio M de Sá Patroni
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Geizecler Tommazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, 82000 Aarhus, Denmark
| | - Alan R Santos-Silva
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP, Brazil
| | - Márcio A Lopes
- Departamento de Diagnóstico Oral, Faculdade de Odontologia de Piracicaba Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP, Brazil
| | - Gilberto de Castro
- Oncologia Clínica, Instituto do Câncer do Estado de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Thaís B Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | | | - Fabio M Squina
- Universidade de Sorocaba, Departamento de Processos Tecnológicos e Ambientais, São Paulo, Brazil
| | - Guilherme P Telles
- Universidade de Campinas, Instituto de Computação, Campinas, São Paulo, Brazil
| | - Adriana F Paes Leme
- Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, São Paulo, Brazil.
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Das S, Tamang JP. Changes in microbial communities and their predictive functionalities during fermentation of toddy, an alcoholic beverage of India. Microbiol Res 2021; 248:126769. [PMID: 33873140 DOI: 10.1016/j.micres.2021.126769] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/07/2021] [Accepted: 04/03/2021] [Indexed: 12/14/2022]
Abstract
Toddy is a traditional mild-alcoholic drink of India, which is produced from fresh palm saps by natural fermentation. We studied the successional changes in bacterial and fungal communities during the natural fermentation (0 h-96 h) of toddy. During fermentation, alcohol content of the fermenting saps increased significantly from 0.6 %±0.15 to 5.6 %±0.02, pH decreased from 6.33 %±0.02-3.93 ± 0.01, volatile and titratable acidity acidity (g/100 mL) increased from 0.17 ± 0.02 (0 h) to 0.48 ± 0.02 (96 h) and 1.30 ± 0.005 (0 h) to 2.47 ± 0.005 (96 h), respectively. Total sugar content and ˚BRIX also decreased during the fermentation. Firmicutes (78.25 %) was the most abundant phylum followed by Proteobacteria (21.57 %). Leuconostoc was the most abundant genus in the early stages of fermentation. However, Lactobacillus and Gluconoacetobacter were found abundant with increase in pH during the later phases of fermentation (72 h-96 h). Ascomycota (99.02 %) was the most abundant fungal phylum. Hanseniaspora was the abundant yeast in the initial stages of fermentation, whereas the population of Saccharomyces increased significantly after 24 h of fermentation. Torulaspora, Lachancea and Starmerella showed their heterogeneous distribution throughout the fermentation. Computational analysis of metagenomes based on KEGG and MetaCyc databases showed different predictive functional profiles such as folate biosynthesis, glutathione metabolism, terpenoids biosynthesis and biosynthesis of amino acids with significant differences between the fresh palm saps and fermenting saps during toddy fermentation.
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Affiliation(s)
- Souvik Das
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India.
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Liu M, Devlin JC, Hu J, Volkova A, Battaglia TW, Ho M, Asplin JR, Byrd A, Loke P, Li H, Ruggles KV, Tsirigos A, Blaser MJ, Nazzal L. Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease. eLife 2021; 10:e63642. [PMID: 33769280 PMCID: PMC8062136 DOI: 10.7554/elife.63642] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Over-accumulation of oxalate in humans may lead to nephrolithiasis and nephrocalcinosis. Humans lack endogenous oxalate degradation pathways (ODP), but intestinal microbes can degrade oxalate using multiple ODPs and protect against its absorption. The exact oxalate-degrading taxa in the human microbiota and their ODP have not been described. We leverage multi-omics data (>3000 samples from >1000 subjects) to show that the human microbiota primarily uses the type II ODP, rather than type I. Furthermore, among the diverse ODP-encoding microbes, an oxalate autotroph, Oxalobacter formigenes, dominates this function transcriptionally. Patients with inflammatory bowel disease (IBD) frequently suffer from disrupted oxalate homeostasis and calcium oxalate nephrolithiasis. We show that the enteric oxalate level is elevated in IBD patients, with highest levels in Crohn's disease (CD) patients with both ileal and colonic involvement consistent with known nephrolithiasis risk. We show that the microbiota ODP expression is reduced in IBD patients, which may contribute to the disrupted oxalate homeostasis. The specific changes in ODP expression by several important taxa suggest that they play distinct roles in IBD-induced nephrolithiasis risk. Lastly, we colonize mice that are maintained in the gnotobiotic facility with O. formigenes, using either a laboratory isolate or an isolate we cultured from human stools, and observed a significant reduction in host fecal and urine oxalate levels, supporting our in silico prediction of the importance of the microbiome, particularly O. formigenes in host oxalate homeostasis.
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Affiliation(s)
- Menghan Liu
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Joseph C Devlin
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | - Jiyuan Hu
- NYU Langone HealthNew YorkUnited States
| | - Angelina Volkova
- NYU Langone HealthNew YorkUnited States
- Vilcek Institute of Graduate Biomedical SciencesNew YorkUnited States
| | | | - Melody Ho
- NYU Langone HealthNew YorkUnited States
| | - John R Asplin
- Litholink Corporation, Laboratory Corporation of America HoldingsChicagoUnited States
| | - Allyson Byrd
- Department of Cancer Immunology, Genentech IncSouth San FranciscoUnited States
| | - P'ng Loke
- NYU Langone HealthNew YorkUnited States
| | - Huilin Li
- NYU Langone HealthNew YorkUnited States
| | | | | | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers UniversityNew YorkUnited States
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Daliri EBM, Ofosu FK, Chelliah R, Lee BH, Oh DH. Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies. Biomolecules 2021; 11:300. [PMID: 33671370 PMCID: PMC7922017 DOI: 10.3390/biom11020300] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
The advent of omic technology has made it possible to identify viable but unculturable micro-organisms in the gut. Therefore, application of multi-omic technologies in gut microbiome studies has become invaluable for unveiling a comprehensive interaction between these commensals in health and disease. Meanwhile, despite the successful identification of many microbial and host-microbial cometabolites that have been reported so far, it remains difficult to clearly identify the origin and function of some proteins and metabolites that are detected in gut samples. However, the application of single omic techniques for studying the gut microbiome comes with its own challenges which may be overcome if a number of different omics techniques are combined. In this review, we discuss our current knowledge about multi-omic techniques, their challenges and future perspective in this field of gut microbiome studies.
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Affiliation(s)
- Eric Banan-Mwine Daliri
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Fred Kwame Ofosu
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Ramachandran Chelliah
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
| | - Byong H. Lee
- SportBiomics, Sacramento Inc., California, CA 95660, USA;
| | - Deog-Hwan Oh
- Department of Food Science and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea; (E.B.-M.D.); (F.K.O.); (R.C.)
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Kharnaior P, Tamang JP. Bacterial and fungal communities and their predictive functional profiles in kinema, a naturally fermented soybean food of India, Nepal and Bhutan. Food Res Int 2021; 140:110055. [PMID: 33648280 DOI: 10.1016/j.foodres.2020.110055] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/21/2022]
Abstract
Bacterial and fungal communities in kinema, a naturally fermented soybean food of the Eastern Himalayan regions of India, Nepal and Bhutan were profiled by high-throughout sequence analysis. Firmicutes (78.4%) was the most abundant phylum in kinema, followed by Proteobacteria (14.76%) and other phyla. Twenty seven species of Bacillus were detected, among which Bacillus subtilis (28.70%) was the most abundant bacterium, followed by B. licheniformis, B. thermoamylovorans, B. cereus, Ignatzschineria larvae, Corynebacterium casei, B. sonorensis, Proteus vulgaris, Brevibacillus borstelensis, Thermoactinomyces vulgaris, Lactobacillus fermentum and Ignatzschineria indica. Ascomycota was the most abundant fungal phylum in kinema. Wallemia canadensis, Penicillium spp., Aspergillus spp., Exobasidium spp., Arthrocladium spp., Aspergillus penicillioides, Mortierella spp., Rhizopus arrhizus and Mucor circinelloides, were major moulds, and Pichia sporocuriosa, Trichosporon spp., Saccharomycopsis malanga and Rhodotorula cycloclastica were abundant yeasts in kinema. We detected 277 species of bacteria among which, 99.09% were culturable and 0.91% were unculturable; and 80 fungal species among which, 33.72% were culturable and 66.28% were unculturable. Several unique bacterial genera to each country were observed, whereas no unique fungal genus was observed in kinema. Maximum coverage of sequencing depth was observed in all samples. Based on PCA plot, close relation was observed between samples of India and Nepal, whereas samples of Bhutan was clearly distinctive. Predictive functional features of bacterial and fungi related to metabolisms were inferred by the KEGG Orthology and MetaCyc databases, respectively.
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Affiliation(s)
- Pynhunlang Kharnaior
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India.
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Ghosh A, Firdous S, Saha S. Bioinformatics for Human Microbiome. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Ongmu Bhutia M, Thapa N, Nakibapher Jones Shangpliang H, Prakash Tamang J. Metataxonomic profiling of bacterial communities and their predictive functional profiles in traditionally preserved meat products of Sikkim state in India. Food Res Int 2020; 140:110002. [PMID: 33648235 DOI: 10.1016/j.foodres.2020.110002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/29/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Traditionally preserved meat products are common food items in Sikkim state of India. We studied the high-throughput sequencing of four traditionally preserved meat products viz. beef kargyong, pork kargyong, yak satchu and khyopeh to profile the bacterial communities and also inferred their predictive functional profiles. Overall abundant OTUs in samples showed that Firmicutes was the abundant phylum followed by Proteobacteria and Bacteroidetes. Abundant species detected in each product were Psychrobacter pulmonis in beef kargyong, Lactobacillus sakei in pork kargyong, Bdellovibrio bacteriovorus and Ignatzschinera sp. in yak satchu and Lactobacillus sakei and Enterococcus sp. in khyopeh. Several genera unique to each product, based on analysis of shared OTUs contents, were observed among the samples except in khyopeh. Goods coverage recorded to 1.0 was observed, which reflected the maximum bacterial diversity in the samples. Alpha diversity metrics showed a maximum bacterial diversity in khyopeh and lowest in pork kargyong Community dissimilarities in the products were observed by PCoA plot. A total of 133 KEGG predictive functional pathways was observed in beef kargyong, 131 in pork kargyong, 125 in yak satchu and 101 in khyopeh. Metagenome contribution of the OTUs was computed using PICTRUSt2 and visualized by BURRITO software to predict the metabolic pathways. Several predictive functional profiles were contributed by abundant OTUs represented by Enterococcus, Acinetobacter, Agrobacterium, Bdellovibrio, Chryseobacterium, Lactococcus, Leuconostoc, Psychrobacter, and Staphylococcus.
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Affiliation(s)
- Meera Ongmu Bhutia
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Namrata Thapa
- Biotech Hub, Department of Zoology, Nar Bahadur Bhandari Degree College, Tadong 737102, Sikkim, India.
| | - H Nakibapher Jones Shangpliang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok 737102, Sikkim, India.
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Abstract
Correction to: J Biosci (2019) 44:119 https://doi.org/10.1007/s12038-019-9933-z In the October 2019 Special Issue of the Journal of Biosciences on Current Trends in Microbiome Research, in the Review article titled "Visual exploration of microbiome data" by Bhusan K. Kuntal and Sharmila S. Mande (DOI: 10.1007/s12038-019-9933-z; Vol. 44, Article No. 119), affiliation 3 for Bhusan K. Kuntal was incorrectly mentioned as "Academy of Scientific and Innovative Research, CSIR-National Chemical Laboratory Campus, Pune 411008, India''. The correct affiliation should read as ''Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India".
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Affiliation(s)
- Bhusan K Kuntal
- Bio-Sciences R and D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune 411 013, India
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Andras JP, Rodriguez-Reillo WG, Truchon A, Blanchard JL, Pierce EA, Ballantine KA. Rewilding the small stuff: the effect of ecological restoration on prokaryotic communities of peatland soils. FEMS Microbiol Ecol 2020; 96:5893291. [PMID: 32804239 DOI: 10.1093/femsec/fiaa144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
To investigate the effect that restoration has on the microbiome of wetland soils, we used 16S amplicon sequencing to characterize the soil prokaryotic communities of retired cranberry farms that were restored to approximate the peat wetlands they once were. For comparison, we also surveyed the soil communities of active cranberry farms, retired cranberry farms and natural peat wetlands that were never farmed. Our results show that the prokaryotic communities of active cranberry farms are distinct from those of natural peat wetlands. Moreover, 4 years after restoration, the prokaryotic community structure of restored cranberry farms had shifted, resulting in a community more similar to natural peat wetlands than to active farms. Meanwhile, the prokaryotic communities of retired cranberry farms remained similar to those of active farms. The observed differences in community structure across site types corresponded with significant differences in inferred capacity for denitrification, methanotrophy and methanogenesis, and community composition was also correlated with previously published patterns of denitrification and carbon sequestration measured from the same soil samples. Taken together, these results suggest that ecological restoration efforts have the potential to restore ecosystem functions of soils and that they do so by 'rewilding' the communities of resident soil microbes.
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Affiliation(s)
- Jason P Andras
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Alexander Truchon
- Biology Department, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Erin A Pierce
- Department of Environmental Studies, Mount Holyoke College, South Hadley, MA, USA
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Hewitt OH, Díez-Vives C, Taboada S. Microbial insights from Antarctic and Mediterranean shallow-water bone-eating worms. Polar Biol 2020. [DOI: 10.1007/s00300-020-02731-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractBone-eating worms of the genus Osedax (Annelida, Siboglinidae) form unique holobionts (functional entity comprising host and associated microbiota), highly adapted to inhabit bone tissue of marine vertebrates. These gutless worms have developed nutritional symbioses housing intracellular, horizontally acquired, heterotrophic bacteria hypothesised to harness nutrients from organic compounds, sequestered within the bone. Despite previous efforts, critical mechanisms mediating activity and acquisition of diverse bacterial assemblages remain unclear. Using 16S rRNA amplicon sequencing, we performed detailed taxonomic and predicted functional analyses shedding light on the microbial communities of two shallow-water Osedax species (Osedax deceptionensis and Osedax ‘mediterranea’) from contrasting habitats (Antarctic and Mediterranean Sea), in two tissue types (roots and palps). Comparative assessments between host species revealed distinct microbial assemblages whilst, within host species and body tissue, relative symbiont frequencies retained high variability. We reported relatively high abundances of microbes previously classified as primary endosymbionts, Ribotype 1 (order Oceanospirillales), and diverse likely secondary epibionts warranting further exploration as recurrent Osedax associates. Surprisingly, O. ‘mediterranea’ exhibited relatively low abundance of Oceanospirillales, but increased abundance of other potentially hydrocarbon degrading bacteria from the family Alteromonadaceae. We hypothesise the presence of functionally similar, non-Oceanospirillales primary endosymbionts within O. ‘mediterranea’. Functional metagenomic profiling (using 16S rRNA sequences) predicted broad metabolic capabilities, encompassing relatively large abundances of genes associated with amino acid metabolism. Comparative analyses between host body tissue communities highlighted several genes potentially providing critical functions to the Osedax host or that confer adaptations for intracellular life, housed within bone embedded host root tissues.
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Secombe KR, Ball IA, Shirren J, Wignall AD, Keefe DM, Bowen JM. Pathophysiology of neratinib-induced diarrhea in male and female rats: microbial alterations a potential determinant. Breast Cancer 2020; 28:99-109. [PMID: 32683606 DOI: 10.1007/s12282-020-01133-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Neratinib is a potent irreversible pan-ErbB tyrosine kinase inhibitor, approved by the FDA for extended adjuvant treatment of HER2-positive breast cancer. Diarrhea is the most frequently observed adverse event with tyrosine kinase inhibitor therapy. In this study, we developed a reproducible model for neratinib-induced diarrhea in male and female rats. METHODS At first, male rats were treated with neratinib at 15, 30 or 50 mg/kg or vehicle control via oral gavage for 28 days (total n = 12). Secondly, we compared outcomes of male (n = 7) and female (n = 8) rats, treated with 50 mg/kg neratinib. RESULTS Rats treated with a 50 mg/kg daily dose of neratinib had a reproducible and clinically relevant level of diarrhea and therefore was confirmed as an appropriate dose. Male rats treated with neratinib had significant changes to their gut microbiome. This included neratinib-induced increases in Ruminococcaceae (P = 0.0023) and Oscillospira (P = 0.026), and decreases in Blautia (P = 0.0002). On average, female rats experienced more significant neratinib-induced diarrhea (mean grade 1.526) compared with male rats (mean grade 1.182) (P < 0.0001). Neratinib caused a reduction in percentage weight gain after 28 days of treatment in females (P = 0.0018) compared with vehicle controls. Females and males both showed instances of villus atrophy and fusion, most severely in the distal ileum. Serum neratinib concentration was higher in female rats compared to male rats (P = 0.043). CONCLUSIONS A reproducible diarrhea model was developed in both female and male rats, which indicated that diarrhea pathogenesis is multifactorial, including anatomical disruption particularly evident in the distal ileum, and alterations in microbial composition.
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Affiliation(s)
- Kate R Secombe
- Adelaide Medical School, University of Adelaide, Level 2 Helen Mayo Building South, Frome Rd, Adelaide, South Australia, 5005, Australia.
| | - Imogen A Ball
- Adelaide Medical School, University of Adelaide, Level 2 Helen Mayo Building South, Frome Rd, Adelaide, South Australia, 5005, Australia
| | - Joseph Shirren
- Adelaide Medical School, University of Adelaide, Level 2 Helen Mayo Building South, Frome Rd, Adelaide, South Australia, 5005, Australia
| | - Anthony D Wignall
- Adelaide Medical School, University of Adelaide, Level 2 Helen Mayo Building South, Frome Rd, Adelaide, South Australia, 5005, Australia
- Division of Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Dorothy M Keefe
- Adelaide Medical School, University of Adelaide, Level 2 Helen Mayo Building South, Frome Rd, Adelaide, South Australia, 5005, Australia
| | - Joanne M Bowen
- Adelaide Medical School, University of Adelaide, Level 2 Helen Mayo Building South, Frome Rd, Adelaide, South Australia, 5005, Australia
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Swarte JC, Eelderink C, Douwes RM, Said MY, Hu S, Post A, Westerhuis R, Bakker SJ, Harmsen HJ. Effect of High versus Low Dairy Consumption on the Gut Microbiome: Results of a Randomized, Cross-Over Study. Nutrients 2020; 12:nu12072129. [PMID: 32708991 PMCID: PMC7400927 DOI: 10.3390/nu12072129] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
The influence of dairy on the gut microbiome has not been studied extensively. We performed a randomized cross-over study to analyze the effect of high dairy intake on the gut microbiome. Subjects were randomly assigned to a high-dairy diet (HDD) (5-6 dairy portions per day) and a low-dairy diet (LDD) (≤1 dairy portion per day) for 6 weeks with a washout period of 4 weeks in between both diets. The gut microbiome was assessed using 16S rRNA gene sequencing. Compositionality and functionality of the gut microbiome was assessed using Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Stool consistency was evaluated using the Bristol stool chart. In total, 46 healthy overweight subjects (BMI range 25-30 kg/m2) completed both intervention periods. During the HDD, there was a significantly higher abundance of the genera Streptococcus, Leuconostoc, and Lactococcus, and the species Streptococcus thermophilus, Erysipelatoclostridium ramosum and Leuconostoc mesenteroides (pFDR < 0.10). Furthermore, during the HDD, there was a significantly lower abundance of the genera Faecalibacterium and Bilophila, and the species Faecalibacterium prausnitzii, Clostridium aldenense, Acetivibrio ethanolgignens, Bilophila wadsworthia and Lactococcus lactis (pFDR < 0.10). There were eight subjects who became constipated during the HDD and these subjects all had a lower abundance of F. prausnitzii. This is the first cross-over study in which the effect of an HDD compared to an LDD on the gut microbiome has been studied. An HDD led to a significantly different composition of the gut microbiome, with a particularly lower abundance of F. prausnitzii and a higher abundance of S. thermophilus. Constipation was observed in several subjects during the HDD. Predicted metabolic pathways were not significantly altered due to an HDD.
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Affiliation(s)
- J. Casper Swarte
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (C.E.); (R.M.D); (M.Y.S.); (A.P.); (S.J.L.B.)
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Correspondence: ; Tel.: +31-(0)-503-613-677
| | - Coby Eelderink
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (C.E.); (R.M.D); (M.Y.S.); (A.P.); (S.J.L.B.)
| | - Rianne M. Douwes
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (C.E.); (R.M.D); (M.Y.S.); (A.P.); (S.J.L.B.)
| | - M. Yusof Said
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (C.E.); (R.M.D); (M.Y.S.); (A.P.); (S.J.L.B.)
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Adrian Post
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (C.E.); (R.M.D); (M.Y.S.); (A.P.); (S.J.L.B.)
| | - Ralf Westerhuis
- Dialyses Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Stephan J.L. Bakker
- Department of Nephrology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (C.E.); (R.M.D); (M.Y.S.); (A.P.); (S.J.L.B.)
| | - Hermie J.M. Harmsen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
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42
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Greslehner GP. Microbiome Structure and Function: A New Framework for Interpreting Data. Bioessays 2020; 42:e1900255. [DOI: 10.1002/bies.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Gregor P. Greslehner
- University of Bordeaux and CNRS – ImmunoConcept UMR5164, 146 rue Léo Saignat Bordeaux 33076 France
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Kaur H, Merchant M, Haque MM, Mande SS. Crosstalk Between Female Gonadal Hormones and Vaginal Microbiota Across Various Phases of Women's Gynecological Lifecycle. Front Microbiol 2020; 11:551. [PMID: 32296412 PMCID: PMC7136476 DOI: 10.3389/fmicb.2020.00551] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/13/2020] [Indexed: 01/02/2023] Open
Abstract
Functional equilibrium between vaginal microbiota and the host is important for maintaining gynecological and reproductive health. Apart from host genetics, infections, changes in diet, life-style and hygiene status are known to affect this delicate state of equilibrium. More importantly, the gonadal hormones strongly influence the overall structure and function of vaginal microbiota. Several studies have attempted to understand (a) the composition of vaginal microbiota in specific stages of women's reproductive cycle as well as in menopause (b) their association with gonadal hormones, and their potential role in manifestation of specific health conditions (from the perspective of cause/consequence). However, a single study that places, in context, the structural variations of the vaginal microbiome across the entire life-span of women's reproductive cycle and during various stages of menopause is currently lacking. With the objective to obtain a holistic overview of the community dynamics of vaginal micro-environment 'across' various stages of women's reproductive and post-reproductive life-cycle, we have performed a meta-analysis of approximately 1,000 vaginal microbiome samples representing various stages of the reproductive cycle and menopausal states. Objectives of this analysis included (a) understanding temporal changes in vaginal community taxonomic structure and composition as women pass through various reproductive and menopausal stages (b) exploring correlations between the levels of female sex hormones with vaginal microbiome diversity (c) analyzing changes in the pattern of community diversity in cases of dysbiotic conditions such as bacterial vaginosis, and viewing the analyzed changes in the context of a healthy state. Results reveal interesting temporal trends with respect to vaginal microbial community diversity and its pattern of correlation with host physiology. Results indicate significant differences in alpha-diversity and overall vaginal microbial community members in various reproductive and post-reproductive phases. In addition to reinforcing the known influence/role of gonadal hormones in maintaining gynecological health, results indicate how hormonal level perturbations cause/contribute to imbalances in vaginal microbiota. The nature of resulting dysbiotic state and its influence on vaginal health is also analyzed and discussed. Results also suggest that elevated vaginal microbial diversity in pregnancy does not necessarily indicate a state of bacterial infection. The study puts forward a hormone-level driven microbiome diversity hypothesis for explaining temporal patterns in vaginal microbial diversity during various stages of women's reproductive cycle and at menopause.
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Affiliation(s)
| | | | | | - Sharmila S. Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
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Misra BB. The Connection and Disconnection Between Microbiome and Metabolome: A Critical Appraisal in Clinical Research. Biol Res Nurs 2020; 22:561-576. [PMID: 32013533 DOI: 10.1177/1099800420903083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Big data-driven omics research has led to a steep rise in investigations involving two of the most functional omes, the metabolome and microbiome. The former is touted as the closest to the phenotype, and the latter is implicated in general well-being and a plethora of human diseases. Although some research publications have integrated the concepts of the two domains, most focus their analyses on evidence solely originating from one or the other. With a growing interest in connecting the microbiome and metabolome in the context of disease, researchers must also appreciate the disconnect between the two domains. In the present review, drawing examples from the current literature, tools, and resources, I discuss the connections between the microbiome and metabolome and highlight challenges and opportunities in linking them together for the basic, translational, clinical, and nursing research communities.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, 12279Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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Singh R, Haque MM, Mande SS. Lifestyle-Induced Microbial Gradients: An Indian Perspective. Front Microbiol 2019; 10:2874. [PMID: 31921052 PMCID: PMC6928055 DOI: 10.3389/fmicb.2019.02874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/28/2019] [Indexed: 02/06/2023] Open
Abstract
Introduction: Urbanization is a globally pervasive trend. Although urban settings provide better access to infrastructure and opportunities, urban lifestyles have certain negative consequences on human health. A number of recent studies have found interesting associations between the structure of human gut microbiota and the prevalence of metabolic conditions characterizing urban populations. The present study attempts to expand the footprint of these investigations to an Indian context. The objectives include elucidating specific patterns and gradients based on resident habitat and lifestyles (i.e., tribal and urban) that characterize gut microbial communities. Methods: Available 16S rRNA sequence datasets corresponding to the gut microbiota of urban and tribal populations from multiple regions of India have been rigorously compared. This analysis was carried out to understand the overall community structure, resident taxa, and their (inferred) functional components as well as their correlations with available meta-information. Results: The gut microbiota of urban and tribal communities are observed to have characteristically different signatures with respect to diversity as well as taxonomic and functional composition. Primarily, the gut microbiota in tribal communities is found to harbor significantly higher species diversity and richness as compared to that in urban populations. In spite of geographical segregation and diet-related differences, gut microbial diversity was not found to differ significantly between tribal groups. Furthermore, while the taxonomic profiles of different tribal communities cluster together irrespective of their geographic location, enterotype analysis indicates that samples from urban communities form two distinct clusters. Taxonomic analysis of samples in one of these clusters reveals the presence of microbes that are common to both urban and tribal cohorts, indicating a probable transient evolutionary state. Prevotella, previously reported to be the dominant genus resident in Indian gut microbiota, is found to have distinct OTUs and strain-specific oligotypes characterizing resident habitats and diet patterns. Certain interesting associations between microbial abundances and specific metadata have also been observed. Overall, urban lifestyle and diet appear to impact the structure and function of gut microbial communities, and the results of this study provide further evidence of this likely detrimental association. Conclusion: This study attempts to analyze, in an Indian context, the impact of urbanization on the human gut microbiota. Overall, the analysis elucidates interesting taxonomic and functional signatures characterizing the evolutionary transition in gut microbiota from tribal to urban.
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Affiliation(s)
- Rashmi Singh
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| | | | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
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Kolbe AR, Castro-Nallar E, Preciado D, Pérez-Losada M. Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses. Front Cell Infect Microbiol 2019; 9:339. [PMID: 31637220 PMCID: PMC6787523 DOI: 10.3389/fcimb.2019.00339] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/18/2019] [Indexed: 11/25/2022] Open
Abstract
Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3–176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.
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Affiliation(s)
- Allison R Kolbe
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC, United States
| | - Eduardo Castro-Nallar
- Facultad de Ciencias de la Vida, Center for Bioinformatics and Integrative Biology, Universidad Andrés Bello, Santiago, Chile
| | - Diego Preciado
- Division of Pediatric Otolaryngology, Sheikh Zayed Institute, Children's National Health System, Washington, DC, United States
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC, United States.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade Do Porto, Vairão, Portugal
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Kuntal BK, Mande SS. Visual exploration of microbiome data. J Biosci 2019; 44:119. [PMID: 31719228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A dramatic increase in large-scale cross-sectional and temporal-level metagenomic experiments has led to an improved understanding of the microbiome and its role in human well-being. Consequently, a plethora of analytical methods has been developed to decipher microbial biomarkers for various diseases, cluster different ecosystems based on microbial content, and infer functional potential of the microbiome as well as analyze its temporal behavior. Development of user-friendly visualization methods and frameworks is necessary to analyze this data and infer taxonomic and functional patterns corresponding to a phenotype. Thus, new methods as well as application of pre-existing ones has gained importance in recent times pertaining to the huge volume of the generated microbiome data. In this review, we present a brief overview of some useful visualization techniques that have significantly enriched microbiome data analytics.
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Affiliation(s)
- Bhusan K Kuntal
- Bio-Sciences R and D Division, TCS Research, Tata Consultancy Services Ltd., 54-B Hadapsar Industrial Estate, Pune 411 013, India
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Tandon D, Haque MM, Gote M, Jain M, Bhaduri A, Dubey AK, Mande SS. A prospective randomized, double-blind, placebo-controlled, dose-response relationship study to investigate efficacy of fructo-oligosaccharides (FOS) on human gut microflora. Sci Rep 2019; 9:5473. [PMID: 30940833 PMCID: PMC6445088 DOI: 10.1038/s41598-019-41837-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/18/2019] [Indexed: 12/16/2022] Open
Abstract
Fructo-oligosaccharides (FOS), a prebiotic supplement, is known for its Bifidogenic capabilities. However, aspects such as effect of variable quantities of FOS intake on gut microbiota, and temporal dynamics of gut microbiota (transitioning through basal, dosage, and follow-up phases) has not been studied in detail. This study investigated these aspects through a randomized, double-blind, placebo-controlled, dose-response relationship study. The study involved 80 participants being administered FOS at three dose levels (2.5, 5, and 10 g/day) or placebo (Maltodextrin 10 g/day) during dosage phase. Microbial DNA extracted from fecal samples collected at 9 intervening time-points was sequenced and analysed. Results indicate that FOS consumption increased the relative abundance of OTUs belonging to Bifidobacterium and Lactobacillus. Interestingly, higher FOS dosage appears to promote, in contrast to Maltodextrin, the selective proliferation of OTUs belonging to Lactobacillus. While consumption of prebiotics increased bacterial diversity, withdrawal led to its reduction. Apart from probiotic bacteria, a significant change was also observed in certain butyrate-producing microbes like Faecalibacterium, Ruminococcus and Oscillospira. The positive impact of FOS on butyrate-producing bacteria and FOS-mediated increased bacterial diversity reinforces the role of prebiotics in conferring beneficial functions to the host.
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Affiliation(s)
- Disha Tandon
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India
| | - Mohammed Monzoorul Haque
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India
| | - Manoj Gote
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India
| | - Manish Jain
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India
| | - Anirban Bhaduri
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India
| | - Ashok Kumar Dubey
- Tata Chemicals Ltd. Innovation Centre, Survey Number 315, Hissa Number 1-14, Ambedveth, Mulshi, Pune, 412 111, Maharashtra, India.
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India.
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Nagpal S, Haque MM, Singh R, Mande SS. iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities. Front Microbiol 2019; 9:3336. [PMID: 30692979 PMCID: PMC6339920 DOI: 10.3389/fmicb.2018.03336] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 12/24/2018] [Indexed: 01/19/2023] Open
Abstract
Background: The objectives of any metagenomic study typically include identification of resident microbes and their relative proportions (taxonomic analysis), profiling functional diversity (functional analysis), and comparing the identified microbes and functions with available metadata (comparative metagenomics). Given the advantage of cost-effectiveness and convenient data-size, amplicon-based sequencing has remained the technology of choice for exploring phylogenetic diversity of an environment. A recent school of thought, employing the existing genome annotation information for inferring functional capacity of an identified microbiome community, has given a promising alternative to Whole Genome Shotgun sequencing for functional analysis. Although a handful of tools are currently available for function inference, their scope, functionality and utility has essentially remained limited. Need for a comprehensive framework that expands upon the existing scope and enables a standardized workflow for function inference, analysis, and visualization, is therefore felt. Methods: We present iVikodak, a multi-modular web-platform that hosts a logically inter-connected repertoire of functional inference and analysis tools, coupled with a comprehensive visualization interface. iVikodak is equipped with microbial co-inhabitance pattern driven published algorithms along with multiple updated databases of various curated microbe-function maps. It also features an advanced task management and result sharing system through introduction of personalized and portable dashboards. Results: In addition to inferring functions from 16S rRNA gene data, iVikodak enables (a) an in-depth analysis of specific functions of interest (b) identification of microbes contributing to various functions (c) microbial interaction patterns through function-driven correlation networks, and (d) simultaneous functional comparison between multiple microbial communities. We have bench-marked iVikodak through multiple case studies and comparisons with existing state of art. We also introduce the concept of a public repository which provides a first of its kind community-driven framework for scientific data analytics, collaboration and sharing in this area of microbiome research. Conclusion: Developed using modern design and task management practices, iVikodak provides a multi-modular, yet inter-operable, one-stop framework, that intends to simplify the entire approach toward inferred function analysis. It is anticipated to serve as a significant value addition to the existing space of functional metagenomics. iVikodak web-server may be freely accessed at https://web.rniapps.net/iVikodak/.
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Affiliation(s)
- Sunil Nagpal
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| | | | - Rashmi Singh
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
| | - Sharmila S Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services, Pune, India
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Kelsey C, Dreisbach C, Alhusen J, Grossmann T. A primer on investigating the role of the microbiome in brain and cognitive development. Dev Psychobiol 2018; 61:341-349. [DOI: 10.1002/dev.21778] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 08/03/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Caroline Kelsey
- Department of Psychology University of Virginia Charlottesville Virginia
| | - Caitlin Dreisbach
- Data Science Institute University of Virginia Charlottesville Virginia
- School of Nursing University of Virginia Charlottesville Virginia
| | - Jeanne Alhusen
- School of Nursing University of Virginia Charlottesville Virginia
| | - Tobias Grossmann
- Department of Psychology University of Virginia Charlottesville Virginia
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