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Reynolds MC, Cadillo-Quiroz H. Microbial DNA sample preservation and possible artifacts for field-based research in remote tropical peatlands. J Microbiol Methods 2024; 224:106997. [PMID: 39009285 DOI: 10.1016/j.mimet.2024.106997] [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: 08/27/2023] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/17/2024]
Abstract
Surveying bacterial and archaeal microbial communities in host and environmental studies requires the collection and storage of samples. Many studies are conducted in distant locations challenging these prerequisites. The use of preserving buffers is an important alternative when lacking access to cryopreservation, however, its effectivity for samples with challenging chemistry or samples that provide opportunities for fast bacterial or archaeal growth upon exposure to an aerobic environment, like peat samples, requires methodological assessment. Here, in combination with an identified optimal DNA extraction kit for peat soil samples, we test the application of several commercial and a homemade preservation buffer and make recommendations on the method that can most effectively preserve a microbiome reflective of the original state. In treatments with a non-optimal buffer or in the absence, we observed notable community shifts beginning as early as three days post-preservation lowering diversity and community evenness, with growth-driven artifacts from a few specific phyla. However other buffers retain a very close composition relative to the original state, and we described several metrics to understand some variation across them. Due to the chemical effects of preservation buffers, it is critical to test their compatibility and reliability to preserve the original bacterial and archaeal community in different environments.
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Affiliation(s)
- Mark C Reynolds
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States; Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, United States; Biodesign Institute, Arizona State University, Tempe, AZ 85287, United States.
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2
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Hale B, Watts C, Conatser M, Brown E, Wijeratne AJ. Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing. ENVIRONMENTAL MICROBIOME 2024; 19:46. [PMID: 38997772 PMCID: PMC11241880 DOI: 10.1186/s40793-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions. RESULTS Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties. CONCLUSIONS This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.
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Affiliation(s)
- Brett Hale
- AgriGro Incorporated, Doniphan, MO, USA
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA
- College of Science and Mathematics, Arkansas State University, State University, AR, USA
| | - Caitlin Watts
- College of Agriculture, Arkansas State University, State University, AR, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew Conatser
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Edward Brown
- College of Agriculture, Arkansas State University, State University, AR, USA
| | - Asela J Wijeratne
- Arkansas Biosciences Institute, Arkansas State University, State University, AR, USA.
- College of Science and Mathematics, Arkansas State University, State University, AR, USA.
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3
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Sané S, Diouara AAM, Coundoul S, Tene SD, Kane A, Wade SF, Tamba A, Diop M, Mbaye MN, Thiam F, Dieng M, Mbengue M, Nguer CM, Sarr AD, Ndao AS, Touré Kane C. A metagenomic assessment of bacterial community in spices sold open-air markets in Saint-Louis, Senegal. Sci Rep 2024; 14:14709. [PMID: 38926602 PMCID: PMC11208442 DOI: 10.1038/s41598-024-65756-0] [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: 04/21/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024] Open
Abstract
Natural spices play an essential role in human nutrition and well-being. However, their processing on different scales can expose them to potential sources of contamination. This study aimed to describe the bacterial community genomic footprint in spices sold in Senegal. Spice samples were collected in August 2022 in Saint-Louis, Senegal. The genomic region coding bacterial 16S rRNA was then amplified and sequenced using Oxford Nanopore Technology (ONT). Sequencing was carried out on two batches of samples, one containing part of the "Local Spices or Herbs" (n = 10), and the other, a mixture of 7 spices, Curcuma, Thyme and the other part of the "Local Spices or Herbs" (n = 39). Results showed high bacterial diversity and the predominance of Escherichia coli and Salmonella enterica in samples, with total reads of 65,744 and 165,325 for the two batches, respectively. The sample category "Homemade mixture of food condiments ", which includes all "Local Spices or Herbs" samples, showed remarkable bacterial diversity. These were followed by Curcuma, a blend of 7 spices and thyme. Also, the different categories of spices studied show similarities in their bacterial composition. These results highlight the microbial community's highly diverse genomic profile, including pathogenic bacteria, in spice samples.
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Affiliation(s)
- Sarbanding Sané
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Abou Abdallah Malick Diouara
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal.
| | - Seynabou Coundoul
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Sophie Déli Tene
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Alé Kane
- Laboratoire des Sciences Biologiques, Agronomiques, Alimentaires et de Modélisation des Systèmes Complexes (LABAAM), UFR S2ATA, Université Gaston Berger, 234, Saint-Louis, Senegal
| | - Serigne Fallou Wade
- École Supérieure des Sciences Agricoles et de l'Alimentation, Université Amadou Makhtar MBOW, Dakar, Senegal
| | - Abdoulaye Tamba
- Institut Supérieur d'Enseignement Professionnel (ISEP), Bignona, Senegal
| | - Mamadou Diop
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Mame Ndew Mbaye
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Fatou Thiam
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Modou Dieng
- Laboratoire d'Analyses et Essais (LAE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | - Malick Mbengue
- Laboratoire de Microbiologie Appliquée et de Génie Industriel, École Supérieure Polytechnique (ESP), Université Cheikh Anta Diop, 5085, Dakar-Fann, Dakar, Senegal
| | - Cheikh Momar Nguer
- Groupe de Recherche Biotechnologies Appliquées & Bioprocédés Environnementaux (GRBA-BE), École Supérieure Polytechnique (ESP), Université Cheikh Anta DIOP, 5085, Dakar-Fann, Dakar, Senegal
| | | | - Ababacar Sadikh Ndao
- Institut de Technologie Nucléaire Appliqué (ITNA), Université Cheikh Anta DIOP, 5005, Dakar, Senegal
| | - Coumba Touré Kane
- Institut de Technologie Nucléaire Appliqué (ITNA), Université Cheikh Anta DIOP, 5005, Dakar, Senegal
- Université Sine Saloum El Hadj Ibrahima Niass (USSEIN), Kaolack 55, Senegal
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4
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Peters BA, Kelly L, Wang T, Loudig O, Rohan TE. The Breast Microbiome in Breast Cancer Risk and Progression: A Narrative Review. Cancer Epidemiol Biomarkers Prev 2024; 33:9-19. [PMID: 37943168 DOI: 10.1158/1055-9965.epi-23-0965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/06/2023] [Accepted: 11/07/2023] [Indexed: 11/10/2023] Open
Abstract
A decade ago, studies in human populations first revealed the existence of a unique microbial community in the breast, a tissue historically viewed as sterile, with microbial origins seeded through the nipple and/or translocation from other body sites. Since then, research efforts have been made to characterize the microbiome in healthy and cancerous breast tissues. The purpose of this review is to summarize the current evidence for the association of the breast microbiome with breast cancer risk and progression. Briefly, while many studies have examined the breast microbiome in patients with breast cancer, and compared it with the microbiome of benign breast disease tissue or normal breast tissue, these studies have varied widely in their sample sizes, methods, and quality of evidence. Thus, while several large and rigorous cross-sectional studies have provided key evidence of an altered microbiome in breast tumors compared with normal adjacent and healthy control tissue, there are few consistent patterns of perturbed microbial taxa. In addition, only one large prospective study has provided evidence of a relationship between the breast tumor microbiota and cancer prognosis. Future research studies featuring large, well-characterized cohorts with prospective follow-up for breast cancer incidence, progression, and response to treatment are warranted.
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Affiliation(s)
- Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Olivier Loudig
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey
| | - Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
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5
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Li B, Liu S, Chen X, Su Y, Pan N, Liao D, Qiao K, Chen Y, Liu Z. Dynamic Changes in the Microbial Composition and Spoilage Characteristics of Refrigerated Large Yellow Croaker ( Larimichthys crocea) during Storage. Foods 2023; 12:3994. [PMID: 37959111 PMCID: PMC10649330 DOI: 10.3390/foods12213994] [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: 10/08/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The quality changes, dynamic changes in microbial composition, and diversity changes in large yellow croaker (Larimichthys crocea) during 4 °C refrigeration were studied using 16S rDNA high-throughput sequencing technology, and the total viable count (TVC), total volatile basic nitrogen (TVB-N), and thiobarbituric acid-reactive substances (TBARS) were determined. The results revealed a consistent increase in TVC, TVB-N, and TBARS levels over time. On the 9th day, TVC reached 7.43 lg/(CFU/g), while on the 15th day, TVB-N exceeded the upper limit for acceptable quality, reaching 42.56 mg/100 g. Based on the 16S rDNA sequencing results, we categorized the storage period into three phases: early storage (0th and 3rd days), middle storage (6th day), and late storage (9th, 12th, and 15th days). As the storage time increased, both the species richness and diversity exhibited a declining trend. The dominant genus identified among the spoilage bacteria in refrigerated large yellow croaker was Pseudomonas, accounting for a high relative abundance of 82.33%. A comparison was carried out of the spoilage-causing ability of three strains of Pseudomonas screened and isolated from the fish at the end of storage, and they were ranked as follows, from strongest to weakest: P. fluorescen, P. lundensis, and P. psychrophila. This study will provide a theoretical basis for extending the shelf life of large yellow croaker.
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Affiliation(s)
- Binbin Li
- Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Shuji Liu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Xiaoting Chen
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Yongchang Su
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Nan Pan
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Dengyuan Liao
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Kun Qiao
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
| | - Yihui Chen
- Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhiyu Liu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, National Research and Development Center for Marine Fish Processing (Xiamen), Fisheries Research Institute of Fujian, Xiamen 361013, China; (X.C.); (Y.S.); (N.P.); (D.L.); (K.Q.); (Z.L.)
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6
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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7
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Qiu M, Xiao X, Xiao Y, Ma J, Yang H, Jiang H, Dong Q, Wang W. Dynamic Changes of Bacterial Communities and Microbial Association Networks in Ready-to-Eat Chicken Meat during Storage. Foods 2022; 11:foods11223733. [PMID: 36429325 PMCID: PMC9689599 DOI: 10.3390/foods11223733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Ready-to-eat (RTE) chicken is a popular food in China, but its lack of food safety due to bacterial contamination remains a concern, and the dynamic changes of microbial association networks during storage are not fully understood. This study investigated the impact of storage time and temperature on bacterial compositions and microbial association networks in RTE chicken using 16S rDNA high-throughput sequencing. The results show that the predominant phyla present in all samples were Proteobacteria and Firmicutes, and the most abundant genera were Weissella, Pseudomonas and Proteus. Increased storage time and temperature decreased the richness and diversity of the microorganisms of the bacterial communities. Higher storage temperatures impacted the bacterial community composition more significantly. Microbial interaction analyses showed 22 positive and 6 negative interactions at 4 °C, 30 positive and 12 negative interactions at 8 °C and 44 positive and 45 negative interactions at 22 °C, indicating an increase in the complexity of interaction networks with an increase in the storage temperature. Enterobacter dominated the interactions during storage at 4 and 22 °C, and Pseudomonas did so at 22 °C. Moreover, interactions between pathogenic and/or spoilage bacteria, such as those between Pseudomonas fragi and Weissella viridescens, Enterobacter unclassified and Proteus unclassified, or those between Enterobacteriaceae unclassified and W.viridescens, were observed. This study provides insight into the process involved in RTE meat spoilage and can aid in improving the quality and safety of RTE meat products to reduce outbreaks of foodborne illness.
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Affiliation(s)
- Mengjia Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xingning Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiele Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Han Jiang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
- Correspondence: (Q.D.); (W.W.)
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, MOA Laboratory of Quality & Safety Risk Assessment for Agro-Products (Hangzhou), Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence: (Q.D.); (W.W.)
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8
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Peters BA, Santoro N, Kaplan RC, Qi Q. Spotlight on the Gut Microbiome in Menopause: Current Insights. Int J Womens Health 2022; 14:1059-1072. [PMID: 35983178 PMCID: PMC9379122 DOI: 10.2147/ijwh.s340491] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
The gut microbiome is an important contributor to human health, shaped by many endogenous and exogenous factors. The gut microbiome displays sexual dimorphism, suggesting influence of sex hormones, and also has been shown to change with aging. Yet, little is known regarding the influence of menopause - a pivotal event of reproductive aging in women - on the gut microbiome. Here, we summarize what is known regarding the interrelationships of female sex hormones and the gut microbiome, and review the available literature on menopause, female sex hormones, and the gut microbiome in humans. Taken together, research suggests that menopause is associated with lower gut microbiome diversity and a shift toward greater similarity to the male gut microbiome, however more research is needed in large study populations to identify replicable patterns in taxa impacted by menopause. Many gaps in knowledge remain, including the role the gut microbiome may play in menopause-related disease risks, and whether menopausal hormone therapy modifies menopause-related change in the gut microbiome. Given the modifiable nature of the gut microbiome, better understanding of its role in menopause-related health will be critical to identify novel opportunities for improvement of peri- and post-menopausal health and well-being.
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Affiliation(s)
- Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nanette Santoro
- Department of Obstetrics and Gynecology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
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9
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Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics. Microbiol Res 2022; 264:127154. [DOI: 10.1016/j.micres.2022.127154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 01/07/2023]
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10
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Wang Q, Song R, Fan S, Coleman JJ, Xu X, Hu X. Diversity of Fusarium community assembly shapes mycotoxin accumulation of diseased wheat heads. Mol Ecol 2022; 32:2504-2518. [PMID: 35844052 DOI: 10.1111/mec.16618] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/18/2022] [Accepted: 07/08/2022] [Indexed: 10/17/2022]
Abstract
Fusarium head blight (FHB) is a major disease worldwide on cultivated cereals, caused by several Fusarium species. FHB can cause not only yield reduction but also accumulation of mycotoxins in the grain contaminating the food supply. Much of the earlier research has focused on Fusarium pathogenesis, conditions required for disease development and toxin accumulation, and FHB management. However, the Fusarium community composition within the micro-habitat of a single diseased wheat head in the field has had limited investigation. Similarly, the relationship between the Fusarium community structure and mycotoxin accumulation within diseased heads remains unclear. In the present study, we investigated the Fusarium community in diseased heads sampled from different geographical sites in China. Several sites in Shandong province formed a transitional region which contained highly variable profiles of Fusarium OTUs, where a single diseased head could contain more than 10 Fusarium OTUs. Mycotoxin accumulation was independent of geographical properties, however, deoxynivalenol, 15-acetyldeoxynivalenol and zearalenone concentrations showed a significant negative correlation with Fusarium diversity on diseased heads while a significant positive correlation between nivalenol concentration and Fusarium diversity was observed. Taken together, the Fusarium OTU diversity within diseased heads in the field significantly influences mycotoxin accumulation, providing an important point to consider in FHB disease management and mycotoxin research.
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Affiliation(s)
- Qiang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Rui Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Sanhong Fan
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Xiangming Xu
- NIAB East Malling Research (EMR), West Malling, Kent, UK
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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11
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Wang L, Rengel Z, Zhang K, Jin K, Lyu Y, Zhang L, Cheng L, Zhang F, Shen J. Ensuring future food security and resource sustainability: insights into the rhizosphere. iScience 2022; 25:104168. [PMID: 35434553 PMCID: PMC9010633 DOI: 10.1016/j.isci.2022.104168] [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] [Indexed: 01/11/2023] Open
Abstract
Feeding the world’s growing population requires continuously increasing crop yields with less fertilizers and agrochemicals on limited land. Focusing on plant belowground traits, especially root-soil-microbe interactions, holds a great promise for overcoming this challenge. The belowground root-soil-microbe interactions are complex and involve a range of physical, chemical, and biological processes that influence nutrient-use efficiency, plant growth and health. Understanding, predicting, and manipulating these rhizosphere processes will enable us to harness the relevant interactions to improve plant productivity and nutrient-use efficiency. Here, we review the recent progress and challenges in root-soil-microbe interactions. We also highlight how root-soil-microbe interactions could be manipulated to ensure food security and resource sustainability in a changing global climate, with an emphasis on reducing our dependence on fertilizers and agrochemicals.
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Affiliation(s)
- Liyang Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Zed Rengel
- Soil Science & Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.,Institute for Adriatic Crops and Karst Reclamation, Split 21000, Croatia
| | - Kai Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Kemo Jin
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Yang Lyu
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Lin Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Lingyun Cheng
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Fusuo Zhang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
| | - Jianbo Shen
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, PR China
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12
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New generation genome sequencing methods. JOURNAL OF SURGERY AND MEDICINE 2022. [DOI: 10.28982/josam.972535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Sun Y, Debeljak P, Obernosterer I. Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. THE ISME JOURNAL 2021; 15:2933-2946. [PMID: 33941887 PMCID: PMC8443675 DOI: 10.1038/s41396-021-00973-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 02/01/2023]
Abstract
Marine microbes are major drivers of all elemental cycles. The processing of organic carbon by heterotrophic prokaryotes is tightly coupled to the availability of the trace element iron in large regions of the Southern Ocean. However, the functional diversity in iron and carbon metabolism within diverse communities remains a major unresolved issue. Using novel Southern Ocean meta-omics resources including 133 metagenome-assembled genomes (MAGs), we show a mosaic of taxonomy-specific ecological strategies in naturally iron-fertilized and high nutrient low chlorophyll (HNLC) waters. Taxonomic profiling revealed apparent community shifts across contrasting nutrient regimes. Community-level and genome-resolved metatranscriptomics evidenced a moderate association between taxonomic affiliations and iron and carbon-related functional roles. Diverse ecological strategies emerged when considering the central metabolic pathways of individual MAGs. Closely related lineages appear to adapt to distinct ecological niches, based on their distribution and gene regulation patterns. Our in-depth observations emphasize the complex interplay between the genetic repertoire of individual taxa and their environment and how this shapes prokaryotic responses to iron and organic carbon availability in the Southern Ocean.
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Affiliation(s)
- Ying Sun
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France.
| | - Pavla Debeljak
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France
- University of Vienna, Department of Functional and Evolutionary Ecology, A-1090, Vienna, Austria
| | - Ingrid Obernosterer
- CNRS, Sorbonne Université, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650, Banyuls/mer, France
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14
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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15
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Xiong W, Jousset A, Li R, Delgado-Baquerizo M, Bahram M, Logares R, Wilden B, de Groot GA, Amacker N, Kowalchuk GA, Shen Q, Geisen S. A global overview of the trophic structure within microbiomes across ecosystems. ENVIRONMENT INTERNATIONAL 2021; 151:106438. [PMID: 33621916 DOI: 10.1016/j.envint.2021.106438] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The colossal project of mapping the microbiome on Earth is rapidly advancing, with a focus on individual microbial groups. However, a global assessment of the associations between predatory protists and their bacterial prey is still missing at a cross-ecosystem level. This knowledge is critical to better understand the importance of top-down links in structuring microbiomes. Here, we examined 38 sequence-based datasets of paired bacterial and protistan taxa, covering 3,178 samples from diverse habitats including freshwater, marine and soils. We show that community profiles of protists and bacteria strongly correlated across and within habitats, with trophic microbiome structures fundamentally differing across habitats. Soils hosted the most heterogenous and diverse microbiomes. Protist communities were dominated by predators in soils and phototrophs in aquatic environments. This led to changes in the ratio of total protists to bacteria richness, which was highest in marine, while that of predatory protists to bacteria was highest in soils. Taxon richness and relative abundance of predatory protists positively correlated with bacterial richness in marine habitats. These links differed between soils, predatory protist richness and the relative abundance of predatory protists positively correlated with bacterial richness in forest and grassland soils, but not in agricultural soils. Our results suggested that anthropogenic pressure affects higher trophic levels more than lower ones leading to a decoupled trophic structure in microbiomes. Together, our cumulative overview of microbiome patterns of bacteria and protists at the global scale revealed major patterns and differences of the trophic structure of microbiomes across Earth's habitats, and show that anthropogenic factors might have negative effects on the trophic structure within microbiomes. Furthermore, the increased impact of anthropogenic factors on especially higher trophic levels suggests that often-observed reduced ecosystem functions in anthropogenic systems might be partly attributed to a reduction of trophic complexity.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China; Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Manuel Delgado-Baquerizo
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Catalonia, Spain
| | - Benjamin Wilden
- University of Bielefeld, Department of Animal Ecology, Konsequenz 45, 33615 Bielefeld, Germany
| | - Gerard Arjen de Groot
- Wageningen Environmental Research, Wageningen University & Research, 6700 AA Wageningen, the Netherlands
| | - Nathalie Amacker
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
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16
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Zhang Y, Sun G, Hu Z, Xing Z, Zhang S, Zhang X. A multiplex bacterial assay using an element-labeled strategy for 16S rRNA detection. Analyst 2021; 145:6821-6825. [PMID: 32857096 DOI: 10.1039/d0an01272f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A multiplex bacterial assay method that combines S1 nuclease pretreatment and ICP-MS-based elemental labels is presented in this work. Six intestinal related bacteria were identified at the species level and quantified simultaneously without isolation culturing. This method could be extended to assay a mixed bacterial community for point-of-care diagnosis.
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Affiliation(s)
- Yuqing Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China.
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17
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Lin Y, Wang L, Xu K, Li K, Ren H. Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics. MICROBIOME 2021; 9:67. [PMID: 33752740 PMCID: PMC7986553 DOI: 10.1186/s40168-021-01016-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/02/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Denitrifying phosphorus removal sludge (DPRS) is widely adopted for nitrogen and phosphorus removal in wastewater treatment but faces threats from heavy metals. However, a lack of understanding of the taxon-specific heavy metal-resistance mechanisms hinders the targeted optimization of DPRS's robustness in nutrient removal. RESULTS We obtained 403 high- or medium-quality metagenome-assembled genomes from DPRS treated by elevating cadmium, nickel, and chromium pressure. Then, the proteomic responses of individual taxa under heavy metal pressures were characterized, with an emphasis on functions involving heavy metal resistance and maintenance of nutrient metabolism. When oxygen availability was constrained by high-concentration heavy metals, comammox Nitrospira overproduced highly oxygen-affinitive hemoglobin and electron-transporting cytochrome c-like proteins, underpinning its ability to enhance oxygen acquisition and utilization. In contrast, Nitrosomonas overexpressed ammonia monooxygenase and nitrite reductase to facilitate the partial nitrification and denitrification process for maintaining nitrogen removal. Comparisons between phosphorus-accumulating organisms (PAOs) demonstrated different heavy metal-resistance mechanisms adopted by Dechloromonas and Candidatus Accumulibacter, despite their high genomic similarities. In particular, Dechloromonas outcompeted the canonical PAO Candidatus Accumulibacter in synthesizing polyphosphate, a potential public good for heavy metal detoxification. The superiority of Dechloromonas in energy utilization, radical elimination, and damaged cell component repair also contributed to its dominance under heavy metal pressures. Moreover, the enrichment analysis revealed that functions involved in extracellular polymeric substance formation, siderophore activity, and heavy metal efflux were significantly overexpressed due to the related activities of specific taxa. CONCLUSIONS Our study demonstrates that heavy metal-resistance mechanisms within a multipartite community are highly heterogeneous between different taxa. These findings provide a fundamental understanding of how the heterogeneity of individual microorganisms contributes to the metabolic versatility and robustness of microbiomes inhabiting dynamic environments, which is vital for manipulating the adaptation of microbial assemblages under adverse environmental stimuli. Video abstract.
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Affiliation(s)
- Yuan Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Liye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Ke Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Kan Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, N.O.163, Xianlin Avenue, Nanjing, Jiangsu People’s Republic of China
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18
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Chok KC, Ng KY, Koh RY, Chye SM. Role of the gut microbiome in Alzheimer's disease. Rev Neurosci 2021; 32:767-789. [PMID: 33725748 DOI: 10.1515/revneuro-2020-0122] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia, affecting millions of individuals each year and this number is expected to significantly increase. The complicated microorganisms residing in human gut are closely associated with our health. Emerging evidence has suggested possible involvement of human gut microbiome in AD. Symbiotic gut microbiomes are known to maintain brain health by modulating host's barriers integrity, metabolic system, immune system, nervous system and endocrine system. However, in the event of gut dysbiosis and barriers disruption, gut pathobionts disrupt homeostasis of the metabolic system, immune system, nervous system, and endocrine system, resulting in deterioration of neurological functions and subsequently promoting development of AD. Multiple therapeutic approaches, such as fecal microbiome transplant, antibiotics, prebiotics, probiotics, symbiotic, and diet are discussed as potential treatment options for AD by manipulating the gut microbiome to reverse pathological alteration in the systems above.
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Affiliation(s)
- Kian Chung Chok
- School of Health Science, International Medical University, 57000Kuala Lumpur, Malaysia
| | - Khuen Yen Ng
- School of Pharmacy, Monash University Malaysia, 47500Selangor, Malaysia
| | - Rhun Yian Koh
- Division of Biomedical Science and Biotechnology, School of Health Science, International Medical University, No. 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000Kuala Lumpur, Malaysia
| | - Soi Moi Chye
- Division of Biomedical Science and Biotechnology, School of Health Science, International Medical University, No. 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000Kuala Lumpur, Malaysia
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19
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20
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Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J, Figeys D. MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1473-1482. [PMID: 32396346 DOI: 10.1021/jasms.0c00083] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains underexplored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed comprehensive software termed MetaLab for the data analysis of metaproteomic data sets. Here, we build an open search workflow within MetaLab for unbiased identification and quantification of unmodified peptides as well as peptides with various PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, metaproteomics from mouse and human gut microbiomes, and modification-specific enriched data sets. Superior accuracy and sensitivity were obtained simultaneously by using our method compared with the traditional closed search strategy.
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Affiliation(s)
- Kai Cheng
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
| | - Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
| | - Bo Liao
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology and Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Ontario, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto M5G 1Z8, Ontario Canada
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21
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Sequencing barcode construction and identification methods based on block error-correction codes. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1580-1592. [PMID: 32303959 DOI: 10.1007/s11427-019-1651-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023]
Abstract
Multiplexed sequencing relies on specific sample labels, the barcodes, to tag DNA fragments belonging to different samples and to separate the output of the sequencers. However, the barcodes are often corrupted by insertion, deletion and substitution errors introduced during sequencing, which may lead to sample misassignment. In this paper, we propose a barcode construction method, which combines a block error-correction code with a predetermined pseudorandom sequence to generate a base sequence for labeling different samples. Furthermore, to identify the corrupted barcodes for assigning reads to their respective samples, we present a soft decision identification method that consists of inner decoding and outer decoding. The inner decoder establishes the hidden Markov model (HMM) for base insertion/deletion estimation with the pseudorandom sequence, and adapts the forward-backward (FB) algorithm to output the soft information of each bit in the block code. The outer decoder performs soft decision decoding using the soft information to effectively correct multiple errors in the barcodes. Simulation results show that the proposed methods are highly robust to high error rates of insertions, deletions and substitutions in the barcodes. In addition, compared with the inner decoding algorithm of the barcodes based on watermarks, the proposed inner decoding algorithm can greatly reduce the decoding complexity.
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22
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McLean C, Kujawinski EB. AutoTuner: High Fidelity and Robust Parameter Selection for Metabolomics Data Processing. Anal Chem 2020; 92:5724-5732. [PMID: 32212641 PMCID: PMC7310949 DOI: 10.1021/acs.analchem.9b04804] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Untargeted
metabolomics experiments provide a snapshot of cellular
metabolism but remain challenging to interpret due to the computational
complexity involved in data processing and analysis. Prior to any
interpretation, raw data must be processed to remove noise and to
align mass-spectral peaks across samples. This step requires selection
of dataset-specific parameters, as erroneous parameters can result
in noise inflation. While several algorithms exist to automate parameter
selection, each depends on gradient descent optimization functions.
In contrast, our new parameter optimization algorithm, AutoTuner,
obtains parameter estimates from raw data in a single step as opposed
to many iterations. Here, we tested the accuracy and the run-time
of AutoTuner in comparison to isotopologue parameter optimization
(IPO), the most commonly used parameter selection tool, and compared
the resulting parameters’ influence on the properties of feature
tables after processing. We performed a Monte Carlo experiment to
test the robustness of AutoTuner parameter selection and found that
AutoTuner generated similar parameter estimates from random subsets
of samples. We conclude that AutoTuner is a desirable alternative
to existing tools, because it is scalable, highly robust, and very
fast (∼100–1000× speed improvement from other algorithms
going from days to minutes). AutoTuner is freely available as an R
package through BioConductor.
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Affiliation(s)
- Craig McLean
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States.,MIT/WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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23
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Bouwens A, Deen J, Vitale R, D’Huys L, Goyvaerts V, Descloux A, Borrenberghs D, Grussmayer K, Lukes T, Camacho R, Su J, Ruckebusch C, Lasser T, Van De Ville D, Hofkens J, Radenovic A, Frans Janssen KP. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. NAR Genom Bioinform 2020; 2:lqz007. [PMID: 33575560 PMCID: PMC7671359 DOI: 10.1093/nargab/lqz007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.
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Affiliation(s)
- Arno Bouwens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jochem Deen
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Raffaele Vitale
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Laurens D’Huys
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Vince Goyvaerts
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Adrien Descloux
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Kristin Grussmayer
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Tomas Lukes
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Rafael Camacho
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Jia Su
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Cyril Ruckebusch
- LASIR CNRS, Université de Lille, 59655 Villeneuve d’Ascq, France
| | - Theo Lasser
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Dimitri Van De Ville
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Center for Neuroprosthetics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department of Radiology and Medical Informatics, Université de Genève, 1205 Genève, Switzerland
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Kaushal M, Mahuku G, Swennen R. Metagenomic Insights of the Root Colonizing Microbiome Associated with Symptomatic and Non-Symptomatic Bananas in Fusarium Wilt Infected Fields. PLANTS 2020; 9:plants9020263. [PMID: 32085593 PMCID: PMC7076721 DOI: 10.3390/plants9020263] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/10/2020] [Accepted: 02/14/2020] [Indexed: 12/25/2022]
Abstract
Plants tissues are colonized by diverse communities of microorganisms called endophytes. They are key determinants of plant production and health, for example by facilitating nutrient exchanges or limiting disease development. Endophytic communities of banana plants have not been studied until very recently, and their potential role in disease development has not been explored so far. Roots from symptomatic and non-symptomatic banana plants were sampled from fields infected by Fusarium oxysporum f.sp. cubense race 1. The goal was to compare the endophytic microbiota between symptomatic and non-symptomatic plants through high throughput sequencing of 16s rDNA and shotgun metagenome sequencing. The results revealed that the endophytic root microbiome in bananas is dominated by Proteobacteria and Bacteroidetes followed to a lesser extent by Actinobacteria. The development of disease greatly impacted the endophytic microbial communities. For example, Flavobacteriales abundance was correlated with symptom development.
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Affiliation(s)
- Manoj Kaushal
- International Institute of Tropical Agriculture (IITA), Mikocheni B, Dar es Salaam-34441, Tanzania;
- Correspondence: ; Tel.: +255-758589012
| | - George Mahuku
- International Institute of Tropical Agriculture (IITA), Mikocheni B, Dar es Salaam-34441, Tanzania;
| | - Rony Swennen
- Bioversity International, Willem De Croylaan 42, B-3001 Leuven, Belgium;
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, B-3001 Leuven, Belgium
- International Institute of Tropical Agriculture. c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), P.O. Box 447, Arusha 23306, Tanzania
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25
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Dong X, Strous M. An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front Genet 2019; 10:999. [PMID: 31681429 PMCID: PMC6803454 DOI: 10.3389/fgene.2019.00999] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/20/2019] [Indexed: 12/16/2022] Open
Abstract
Here, we describe MetaErg, a standalone and fully automated metagenome and metaproteome annotation pipeline. Annotation of metagenomes is challenging. First, metagenomes contain sequence data of many organisms from all domains of life. Second, many of these are from understudied lineages, encoding genes with low similarity to experimentally validated reference genes. Third, assembly and binning are not perfect, sometimes resulting in artifactual hybrid contigs or genomes. To address these challenges, MetaErg provides graphical summaries of annotation outcomes, both for the complete metagenome and for individual metagenome-assembled genomes (MAGs). It performs a comprehensive annotation of each gene, including taxonomic classification, enabling functional inferences despite low similarity to reference genes, as well as detection of potential assembly or binning artifacts. When provided with metaproteome information, it visualizes gene and pathway activity using sequencing coverage and proteomic spectral counts, respectively. For visualization, MetaErg provides an HTML interface, bringing all annotation results together, and producing sortable and searchable tables, collapsible trees, and other graphic representations enabling intuitive navigation of complex data. MetaErg, implemented in Perl, HTML, and JavaScript, is a fully open source application, distributed under Academic Free License at https://github.com/xiaoli-dong/metaerg. MetaErg is also available as a docker image at https://hub.docker.com/r/xiaolidong/docker-metaerg.
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Affiliation(s)
- Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
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26
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Kumar M, Ji B, Zengler K, Nielsen J. Modelling approaches for studying the microbiome. Nat Microbiol 2019; 4:1253-1267. [PMID: 31337891 DOI: 10.1038/s41564-019-0491-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/21/2019] [Indexed: 02/08/2023]
Abstract
Advances in metagenome sequencing of the human microbiome have provided a plethora of new insights and revealed a close association of this complex ecosystem with a range of human diseases. However, there is little knowledge about how the different members of the microbial community interact with each other and with the host, and we lack basic mechanistic understanding of these interactions related to health and disease. Mathematical modelling has been demonstrated to be highly advantageous for gaining insights into the dynamics and interactions of complex systems and in recent years, several modelling approaches have been proposed to enhance our understanding of the microbiome. Here, we review the latest developments and current approaches, and highlight how different modelling strategies have been applied to unravel the highly dynamic nature of the human microbiome. Furthermore, we discuss present limitations of different modelling strategies and provide a perspective of how modelling can advance understanding and offer new treatment routes to impact human health.
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Affiliation(s)
- Manish Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Department of Pediatrics, University of California, San Diego, CA, USA
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, USA.,Department of Bioengineering, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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27
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Hernandez-Valladares M, Wangen R, Berven FS, Guldbrandsen A. Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action. Curr Med Chem 2019; 26:5317-5337. [PMID: 31241430 DOI: 10.2174/0929867326666190503164004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/23/2018] [Accepted: 02/01/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological environment that PTM crosstalk studies can describe. Besides gene expression and phosphorylation profiling of acute myeloid leukemia (AML) samples, the functional combination of several PTMs that might contribute to a better understanding of the complexity of the AML proteome remains to be discovered. OBJECTIVE By reviewing current workflows for the simultaneous enrichment of several PTMs and bioinformatics tools to analyze mass spectrometry (MS)-based data, our major objective is to introduce the PTM crosstalk field to the AML research community. RESULTS After an introduction to PTMs and PTM crosstalk, this review introduces several protocols for the simultaneous enrichment of PTMs. Two of them allow a simultaneous enrichment of at least three PTMs when using 0.5-2 mg of cell lysate. We have reviewed many of the bioinformatics tools used for PTM crosstalk discovery as its complex data analysis, mainly generated from MS, becomes challenging for most AML researchers. We have presented several non-AML PTM crosstalk studies throughout the review in order to show how important the characterization of PTM crosstalk becomes for the selection of disease biomarkers and therapeutic targets. CONCLUSION Herein, we have reviewed the advances and pitfalls of the emerging PTM crosstalk field and its potential contribution to unravel the heterogeneity of AML. The complexity of sample preparation and bioinformatics workflows demands a good interaction between experts of several areas.
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021 Bergen, Norway.,The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Rebecca Wangen
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Jonas Lies vei 87, N-5021 Bergen, Norway.,The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.,Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Jonas Lies vei 65, N-5021 Bergen, Norway
| | - Frode S Berven
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Astrid Guldbrandsen
- The Proteomics Unit at the University of Bergen, Department of Biomedicine, Building for Basic Biology, Faculty of Medicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.,Computational Biology Unit, Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Bergen, Thormøhlensgt 55, N-5008 Bergen, Norway
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28
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Methods for extracting 'omes from microbialites. J Microbiol Methods 2019; 160:1-10. [PMID: 30877015 DOI: 10.1016/j.mimet.2019.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 11/20/2022]
Abstract
Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.
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RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids. mSystems 2019; 4:mSystems00349-18. [PMID: 30834332 PMCID: PMC6392096 DOI: 10.1128/msystems.00349-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/29/2019] [Indexed: 12/01/2022] Open
Abstract
Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes. Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.
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30
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Delafont V, Perrin Y, Bouchon D, Moulin L, Héchard Y. Targeted Metagenomics of Microbial Diversity in Free-Living Amoebae and Water Samples. Methods Mol Biol 2019; 1921:421-428. [PMID: 30694507 DOI: 10.1007/978-1-4939-9048-1_26] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The presence of Legionella spp. in natural and man-made water systems is a great public health concern and heavily depends on the presence of free-living amoebae. Taking advantage of the development and affordability of next-generation sequencing technology, we present here a method to characterize the whole bacterial community directly from water samples, as well as from isolated free-living amoebae.
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Affiliation(s)
- Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France
| | - Yoann Perrin
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, Ivry sur Seine, France
| | - Didier Bouchon
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l'Eau, R&D Biologie, Ivry sur Seine, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions, Equipes "Microbiologie de l'Eau" et "Ecologie, Evolution, Symbiose", Université de Poitiers, UMR CNRS 7267, Poitiers, France.
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31
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White RA, Gavelis G, Soles SA, Gosselin E, Slater GF, Lim DSS, Leander B, Suttle CA. The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress. Front Microbiol 2018; 9:2180. [PMID: 30374333 PMCID: PMC6196244 DOI: 10.3389/fmicb.2018.02180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 08/24/2018] [Indexed: 12/15/2022] Open
Abstract
Members of the bacterial genus Agrococcus are globally distributed and found across environments so highly diverse that they include forests, deserts, and coal mines, as well as in potatoes and cheese. Despite how widely Agrococcus occurs, the extent of its physiology, genomes, and potential roles in the environment are poorly understood. Here we use whole-genome analysis, chemotaxonomic markers, morphology, and 16S rRNA gene phylogeny to describe a new isolate of the genus Agrococcus from freshwater microbialites in Pavilion Lake, British Columbia, Canada. We characterize this isolate as a new species Agrococcus pavilionensis strain RW1 and provide the first complete genome from a member of the genus Agrococcus. The A. pavilionensis genome consists of one chromosome (2,627,177 bp) as well as two plasmids (HC-CG1 1,427 bp, and LC-RRW783 31,795 bp). The genome reveals considerable genetic promiscuity via mobile elements, including a prophage and plasmids involved in integration, transposition, and heavy-metal stress. A. pavilionensis strain RW1 differs from other members of the Agrococcus genus by having a novel phospholipid fatty acid iso-C15:1Δ4, β-galactosidase activity and amygdalin utilization. Carotenoid biosynthesis is predicted by genomic metabolic reconstruction, which explains the characteristic yellow pigmentation of A. pavilionensis. Metabolic reconstructions of strain RW1 genome predicts a pathway for releasing ammonia via ammonification amino acids, which could increase the saturation index leading to carbonate precipitation. Our genomic analyses suggest signatures of environmental adaption to the relatively cold and oligotrophic conditions of Pavilion Lake microbialites. A. pavilionensis strain RW1 in modern microbialites has an ecological significance in Pavilion Lake microbialites, which include potential roles in heavy-metal cycling and carbonate precipitation (e.g., ammonification of amino acids and filamentation which many trap carbonate minerals).
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Affiliation(s)
- Richard Allen White
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Greg Gavelis
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Sarah A Soles
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Emma Gosselin
- Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Greg F Slater
- School of Geography and Earth Sciences, McMaster University, Hamilton, ON, Canada
| | - Darlene S S Lim
- Bay Area Environmental Research Institute, Petaluma, CA, United States.,NASA Ames Research Center, Moffett Field, CA, United States
| | - Brian Leander
- Bay Area Environmental Research Institute, Petaluma, CA, United States
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada.,Department of Earth, Ocean and Atmospheric Sciences, The University of British Columbia, Vancouver, BC, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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32
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Lin H, He QY, Shi L, Sleeman M, Baker MS, Nice EC. Proteomics and the microbiome: pitfalls and potential. Expert Rev Proteomics 2018; 16:501-511. [PMID: 30223687 DOI: 10.1080/14789450.2018.1523724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.
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Affiliation(s)
- Huafeng Lin
- a Department of Biotechnology , College of Life Science and Technology, Jinan University , Guangzhou , Guangdong , China.,b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Qing-Yu He
- c Institute of Life and Health Engineering, College of Life Science and Technology , Jinan University , Guangzhou , China
| | - Lei Shi
- b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Mark Sleeman
- d Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Mark S Baker
- e Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Edouard C Nice
- f Department of Biochemistry and Molecular Biology , Monash University , Melbourne , Victoria , Australia
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33
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Qiao H, Zhang X, Shi H, Song Y, Bian C, Guo A. Assessment of the physicochemical properties and bacterial composition of Lactobacillus plantarum and Enterococcus faecium-fermented Astragalus membranaceus using single molecule, real-time sequencing technology. Sci Rep 2018; 8:11862. [PMID: 30089930 PMCID: PMC6082834 DOI: 10.1038/s41598-018-30288-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
We investigated if fermentation with probiotic cultures could improve the production of health-promoting biological compounds in Astragalus membranaceus. We tested the probiotics Enterococcus faecium, Lactobacillus plantarum and Enterococcus faecium + Lactobacillus plantarum and applied PacBio single molecule, real-time sequencing technology (SMRT) to evaluate the quality of Astragalus fermentation. We found that the production rates of acetic acid, methylacetic acid, aethyl acetic acid and lactic acid using E. faecium + L. plantarum were 1866.24 mg/kg on day 15, 203.80 mg/kg on day 30, 996.04 mg/kg on day 15, and 3081.99 mg/kg on day 20, respectively. Other production rates were: polysaccharides, 9.43%, 8.51%, and 7.59% on day 10; saponins, 19.6912 mg/g, 21.6630 mg/g and 20.2084 mg/g on day 15; and flavonoids, 1.9032 mg/g, 2.0835 mg/g, and 1.7086 mg/g on day 20 using E. faecium, L. plantarum and E. faecium + L. plantarum, respectively. SMRT was used to analyze microbial composition, and we found that E. faecium and L. plantarum were the most prevalent species after fermentation for 3 days. E. faecium + L. plantarum gave more positive effects than single strains in the Astragalus solid state fermentation process. Our data demonstrated that the SMRT sequencing platform is applicable to quality assessment of Astragalus fermentation.
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Affiliation(s)
- Hongxing Qiao
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.,College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Xiaojing Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Hongtao Shi
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Yuzhen Song
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Chuanzhou Bian
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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34
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Koo H, Hakim JA, Morrow CD, Crowley MR, Andersen DT, Bej AK. Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems. Life (Basel) 2018; 8:life8030029. [PMID: 29997353 PMCID: PMC6161096 DOI: 10.3390/life8030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 11/16/2022] Open
Abstract
This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus, Anaeromyxobacter, Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes. Among CIPs, genes necessary for DNA replication, translation initiation, and transcription termination were highly abundant in all metagenomes. However, genes for fatty acid desaturase (FAD) and trehalose synthase (TS) were common in the soil and lake sediment metagenomes. Interestingly, the Lake Untersee water and sediment metagenome samples contained histone-like nucleoid structuring protein (H-NS) and all genes for CIPs. As for the CASPs, high abundances of a wide range of genes for cryo- and osmo-protectants (glutamate, glycine, choline, and betaine) were identified in all metagenomes. However, genes for exopolysaccharide biosynthesis were dominant in Lake Untersee water, sediment, and other soil metagenomes. The results from this study indicate that although diverse microbial communities are present in various metagenomes, they share common cold-responsive stress genes necessary for their survival and sustenance in the extreme Antarctic conditions.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, California, CA 94043, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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35
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The soil microbiome-from metagenomics to metaphenomics. Curr Opin Microbiol 2018; 43:162-168. [PMID: 29454931 DOI: 10.1016/j.mib.2018.01.013] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 11/21/2022]
Abstract
Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources. Here we describe examples of opportunities towards gaining understanding of the soil metaphenome.
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Li J, Riaz Rajoka MS, Shao D, Jiang C, Jin M, Huang Q, Yang H, Shi J. Strategies to increase the efficacy of using gut microbiota for the modulation of obesity. Obes Rev 2017; 18:1260-1271. [PMID: 28742949 DOI: 10.1111/obr.12590] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/03/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022]
Abstract
Obesity is one of the most serious global public health challenges of the 21st century. The adjustment of gut microbiota is often recommended as an efficient strategy to treat obesity. This modulation of gut microbiota can be performed by many methods, including dietary intervention, antibiotic application, the use of prebiotics and probiotics, bariatric surgery and faecal microbiota transplantation. In most cases, positive effects have been observed in response to treatment, but invalid and even contrary effects have also been observed in some cases due to factors that are unrelated to intervention methods, such as genetic factors, patient age or gender, environmental microbiota, climate, geography and lifestyle. These factors can cause variation of gut microbial populations and thus should also be taken into consideration when selecting modulation strategies.
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Affiliation(s)
- J Li
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - M S Riaz Rajoka
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - D Shao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - C Jiang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - M Jin
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - Q Huang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - H Yang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
| | - J Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Shaanxi, People's Republic of China
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Zhai P, Yang L, Guo X, Wang Z, Guo J, Wang X, Zhu H. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. BMC Bioinformatics 2017; 18:434. [PMID: 28969605 PMCID: PMC5625784 DOI: 10.1186/s12859-017-1849-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/21/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. RESULTS We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. CONCLUSION MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis. Moreover, since the automatically chosen two-group sample test is verified to be outperformed, MetaComp is friendly to users without adequate statistical training. These improvements are aiming to overcome the new challenges under big data era for all meta-omics data. MetaComp is available at: http://cqb.pku.edu.cn/ZhuLab/MetaComp/ and https://github.com/pzhaipku/MetaComp/ .
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Affiliation(s)
- Peng Zhai
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871 China
| | - Longshu Yang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871 China
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
| | - Xiao Guo
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
| | - Zhe Wang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871 China
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
| | - Jiangtao Guo
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871 China
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
| | - Xiaoqi Wang
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871 China
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871 China
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
- Center for Protein Science, Peking University, Beijing, 100871 China
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McCann JC, Elolimy AA, Loor JJ. Rumen Microbiome, Probiotics, and Fermentation Additives. Vet Clin North Am Food Anim Pract 2017; 33:539-553. [PMID: 28764865 DOI: 10.1016/j.cvfa.2017.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Fermentation of a variety of feedstuffs by the ruminal microbiome is the distinctive feature of the ruminant digestive tract. The host derives energy and nutrients from microbiome activity; these organisms are essential to survival. Advances in DNA sequencing and bioinformatics have redefined the rumen microbial community. Current research seeks to connect our understanding of the rumen microbiome with nutritional strategies in ruminant livestock systems and their associated digestive disorders. These efforts align with a growing number of products designed to improve ruminal fermentation to benefit the overall efficiency of ruminant livestock production and health.
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Affiliation(s)
- Joshua C McCann
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA.
| | - Ahmed A Elolimy
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA
| | - Juan J Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA.
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Aksenov AA, da Silva R, Knight R, Lopes NP, Dorrestein PC. Global chemical analysis of biology by mass spectrometry. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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