1
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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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2
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Qiu Z, Yuan L, Lian CA, Lin B, Chen J, Mu R, Qiao X, Zhang L, Xu Z, Fan L, Zhang Y, Wang S, Li J, Cao H, Li B, Chen B, Song C, Liu Y, Shi L, Tian Y, Ni J, Zhang T, Zhou J, Zhuang WQ, Yu K. BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. Nat Commun 2024; 15:2179. [PMID: 38467684 PMCID: PMC10928208 DOI: 10.1038/s41467-024-46539-7] [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: 03/10/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Li Yuan
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
| | - Bin Lin
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
| | - Jie Chen
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Liyu Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Zheng Xu
- Southern University of Sciences and Technology Yantian Hospital, Shenzhen, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Lu Fan
- Department of Ocean Science and Engineering, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Junyi Li
- School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China
| | - Huiluo Cao
- Department of Microbiology, University of Hong Kong, Hong Kong, China
| | - Bing Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Wuhan Benagen Technology Co., Ltd, Wuhan, China
| | - Yongxin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lili Shi
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yonghong Tian
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China
- School of Electronic and Computer Engineering, Peking University, Shenzhen, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Jinren Ni
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, China
| | - Tong Zhang
- Department of Civil Engineering, University of Hong Kong, Hong Kong, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Wei-Qin Zhuang
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Auckland, Auckland, New Zealand
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, China.
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3
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Suazo KF, Mishra V, Maity S, Auger SA, Justyna K, Petre A, Ottoboni L, Ongaro J, Corti SP, Lotti F, Przedborski S, Distefano MD. Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583211. [PMID: 38496415 PMCID: PMC10942399 DOI: 10.1101/2024.03.03.583211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Protein prenylation is one example of a broad class of post-translational modifications where proteins are covalently linked to various hydrophobic moieties. To globally identify and monitor levels of all prenylated proteins in a cell simultaneously, our laboratory and others have developed chemical proteomic approaches that rely on the metabolic incorporation of isoprenoid analogues bearing bio-orthogonal functionality followed by enrichment and subsequent quantitative proteomic analysis. Here, several improvements in the synthesis of the alkyne-containing isoprenoid analogue C15AlkOPP are reported to improve synthetic efficiency. Next, metabolic labeling with C15AlkOPP was optimized to obtain useful levels of metabolic incorporation of the probe in several types of primary cells. Those conditions were then used to study the prenylomes of motor neurons (ES-MNs), astrocytes (ES-As), and their embryonic stem cell progenitors (ESCs), which allowed for the identification of 54 prenylated proteins from ESCs, 50 from ES-MNs and 84 from ES-As, representing all types of prenylation. Bioinformatic analysis revealed specific enriched pathways, including nervous system development, chemokine signaling, Rho GTPase signaling, and adhesion. Hierarchical clustering showed that most enriched pathways in all three cell types are related to GTPase activity and vesicular transport. In contrast, STRING analysis showed significant interactions in two populations that appear to be cell type dependent. The data provided herein demonstrates that robust incorporation of C15AlkOPP can be obtained in ES-MNs and related primary cells purified via magnetic-activated cell sorting allowing the identification and quantification of numerous prenylated proteins. These results suggest that metabolic labeling with C15AlkOPP should be an effective approach for investigating the role of prenylated proteins in primary cells in both normal cells and disease pathologies, including ALS.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Vartika Mishra
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Alex Petre
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Jessica Ongaro
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania P Corti
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032
| | - Serge Przedborski
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Neuroscience, Pathology, and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
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4
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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5
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Sun S, Chen W, Peng K, Chen X, Chen J. Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20970-20982. [PMID: 38383926 PMCID: PMC10948491 DOI: 10.1007/s11356-024-32362-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.
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Affiliation(s)
- Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Wanqi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Kailin Peng
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xueyingzi Chen
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jinju Chen
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Materials, Loughborough University, Loughborough, LE11 3TU, UK.
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6
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Yegin Z, Mamatova Z, Yurt MNZ, Tasbasi BB, Acar EE, Ucak S, Süleymanoğlu AA, Aydin A, Ozalp VC, Sudagidan M. A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan. Chem Biodivers 2024; 21:e202301374. [PMID: 38230544 DOI: 10.1002/cbdv.202301374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/18/2024]
Abstract
Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties.
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Affiliation(s)
- Zeynep Yegin
- Medical Laboratory Techniques Program, Vocational School of Health Services, Sinop University, 57000, Sinop, Türkiye
| | - Zhanylbubu Mamatova
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Türkiye
| | - Mediha Nur Zafer Yurt
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
| | - Behiye Busra Tasbasi
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
| | - Elif Esma Acar
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
| | - Samet Ucak
- Department of Medical Biology and Genetics, School of Medicine, Istanbul Aydin University, Kucukcekmece, 34295, Istanbul, Türkiye
| | - Ali Anıl Süleymanoğlu
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Türkiye
| | - Ali Aydin
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Avcilar, 34320, Istanbul, Türkiye
| | - Veli Cengiz Ozalp
- Department of Medical Biology, Faculty of Medicine, Atilim University, 06830, Ankara, Türkiye
| | - Mert Sudagidan
- KIT-ARGEM R&D Center, Konya Food and Agriculture University, Meram, 42080, Konya, Türkiye
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Behera S, Catreux S, Rossi M, Truong S, Huang Z, Ruehle M, Visvanath A, Parnaby G, Roddey C, Onuchic V, Cameron DL, English A, Mehtalia S, Han J, Mehio R, Sedlazeck FJ. Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573821. [PMID: 38260545 PMCID: PMC10802302 DOI: 10.1101/2024.01.02.573821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Research and medical genomics require comprehensive and scalable solutions to drive the discovery of novel disease targets, evolutionary drivers, and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size (e.g., SNV/SV) or location (e.g., repeats). Here we present DRAGEN that utilizes novel methods based on multigenomes, hardware acceleration, and machine learning based variant detection to provide novel insights into individual genomes with ~30min computation time (from raw reads to variant detection). DRAGEN outperforms all other state-of-the-art methods in speed and accuracy across all variant types (SNV, indel, STR, SV, CNV) and further incorporates specialized methods to obtain key insights in medically relevant genes (e.g., HLA, SMN, GBA). We showcase DRAGEN across 3,202 genomes and demonstrate its scalability, accuracy, and innovations to further advance the integration of comprehensive genomics for research and medical applications.
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Affiliation(s)
- Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | | | | | | | | | | | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, TX, USA
- Department of Computer Science, Rice University, TX, USA
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8
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Eiamsam-Ang T, Tadee P, Buddhasiri S, Chuammitri P, Kittiwan N, Pascoe B, Patchanee P. Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes. J Med Microbiol 2024; 73. [PMID: 38230911 DOI: 10.1099/jmm.0.001787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024] Open
Abstract
Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.
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Affiliation(s)
- Thanaporn Eiamsam-Ang
- Graduate Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Pakpoom Tadee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Songphon Buddhasiri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Phongsakorn Chuammitri
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
| | - Nattinee Kittiwan
- Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang, Thailand
| | - Ben Pascoe
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
- Ineos Oxford Istitute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Prapas Patchanee
- Veterinary Academic Office, Faculty of Veterinary Medicine, Chiang Mai University, Muang, Chiang Mai, Thailand
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9
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Xia Y. Statistical normalization methods in microbiome data with application to microbiome cancer research. Gut Microbes 2023; 15:2244139. [PMID: 37622724 PMCID: PMC10461514 DOI: 10.1080/19490976.2023.2244139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Mounting evidence has shown that gut microbiome is associated with various cancers, including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have unique characteristics and pose major challenges when using standard statistical methods causing results to be invalid or misleading. Thus, to analyze microbiome data, it not only needs appropriate statistical methods, but also requires microbiome data to be normalized prior to statistical analysis. Here, we first describe the unique characteristics of microbiome data and the challenges in analyzing them (Section 2). Then, we provide an overall review on the available normalization methods of 16S rRNA and shotgun metagenomic data along with examples of their applications in microbiome cancer research (Section 3). In Section 4, we comprehensively investigate how the normalization methods of 16S rRNA and shotgun metagenomic data are evaluated. Finally, we summarize and conclude with remarks on statistical normalization methods (Section 5). Altogether, this review aims to provide a broad and comprehensive view and remarks on the promises and challenges of the statistical normalization methods in microbiome data with microbiome cancer research examples.
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Affiliation(s)
- Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, USA
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10
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Amon CER, Fossou RK, Ebou AET, Koua DK, Kouadjo CG, Brou YC, Voko Bi DRR, Cowan DA, Zézé A. The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones. Front Microbiol 2023; 14:1220655. [PMID: 37692382 PMCID: PMC10483230 DOI: 10.3389/fmicb.2023.1220655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.
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Affiliation(s)
- Chiguié Estelle Raïssa Amon
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Romain Kouakou Fossou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Anicet E. T. Ebou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Dominiqueua K. Koua
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Claude Ghislaine Kouadjo
- Laboratoire Central de Biotechnologies, Centre National de la Recherche Agronomique, Abidjan, Côte d’Ivoire
| | - Yao Casimir Brou
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Don Rodrigue Rosin Voko Bi
- Unité de Formation et de Recherche en Agroforesterie, Université Jean Lorougnon Guédé, Daloa, Côte d’Ivoire
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Adolphe Zézé
- Laboratoire de Biotechnologies Végétale et Microbienne, UMRI Sciences Agronomiques et Génie rural, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
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11
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Yancey CE, Kiledal EA, Chaganti SR, Denef VJ, Errera RM, Evans JT, Hart LN, Isailovic D, James WS, Kharbush JJ, Kimbrel JA, Li W, Mayali X, Nitschky H, Polik CA, Powers MA, Premathilaka SH, Rappuhn NA, Reitz LA, Rivera SR, Zwiers CC, Dick GJ. The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. HARMFUL ALGAE 2023; 126:102440. [PMID: 37290887 DOI: 10.1016/j.hal.2023.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.
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Affiliation(s)
- Colleen E Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - E Anders Kiledal
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Vincent J Denef
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Reagan M Errera
- National Oceanic and Atmospheric Administration (NOAA), Great Lakes Environmental Research Laboratory (GLERL), 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Jacob T Evans
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Lauren N Hart
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, United States of America; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - William S James
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jenan J Kharbush
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Helena Nitschky
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Catherine A Polik
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - McKenzie A Powers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - Nicole A Rappuhn
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Laura A Reitz
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sara R Rivera
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Claire C Zwiers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Gregory J Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America.
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12
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Papalamprou A, Yu V, Jiang W, Sheyn J, Stefanovic T, Chen A, Castaneda C, Chavez M, Sheyn D. Single Cell Transcriptomics-Informed Induced Pluripotent Stem Cells Differentiation to Tenogenic Lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536240. [PMID: 37090543 PMCID: PMC10120682 DOI: 10.1101/2023.04.10.536240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
During vertebrate embryogenesis, axial tendons develop from the paraxial mesoderm and differentiate through specific developmental stages to reach the syndetome stage. While the main roles of signaling pathways in the earlier stages of the differentiation have been well established, pathway nuances in syndetome specification from the sclerotome stage have yet to be explored. Here, we show stepwise differentiation of human iPSCs to the syndetome stage using chemically defined media and small molecules that were modified based on single cell RNA-sequencing and pathway analysis. We identified a significant population of branching off-target cells differentiating towards a neural phenotype overexpressing Wnt. Further transcriptomics post-addition of a WNT inhibitor at the somite stage and onwards revealed not only total removal of the neural off-target cells, but also increased syndetome induction efficiency. Fine-tuning tendon differentiation in vitro is essential to address the current challenges in developing a successful cell-based tendon therapy.
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Affiliation(s)
- Angela Papalamprou
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Victoria Yu
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Wensen Jiang
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Julia Sheyn
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Tina Stefanovic
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Angel Chen
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Chloe Castaneda
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Melissa Chavez
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Dmitriy Sheyn
- Orthopaedic Stem Cell Research Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Orthopedics, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
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13
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Wirth R, Bagi Z, Shetty P, Szuhaj M, Cheung TTS, Kovács KL, Maróti G. Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants. THE ISME JOURNAL 2023:10.1038/s41396-023-01448-3. [PMID: 37286740 DOI: 10.1038/s41396-023-01448-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.
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Affiliation(s)
- Roland Wirth
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | | | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.
- Faculty of Water Sciences, University of Public Service, Baja, Hungary.
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14
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Anand U, Dey S, Bontempi E, Ducoli S, Vethaak AD, Dey A, Federici S. Biotechnological methods to remove microplastics: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:1787-1810. [PMID: 36785620 PMCID: PMC9907217 DOI: 10.1007/s10311-022-01552-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/25/2022] [Indexed: 05/14/2023]
Abstract
Microplastics pollution is major threat to ecosystems and is impacting abiotic and biotic components. Microplastics are diverse and highly complex contaminants that transport other contaminants and microbes. Current methods to remove microplastics include biodegradation, incineration, landfilling, and recycling. Here we review microplastics with focus on sources, toxicity, and biodegradation. We discuss the role of algae, fungi, bacteria in the biodegradation, and we present biotechnological methods to enhance degradation, e.g., gene editing tools and bioinformatics.
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Affiliation(s)
- Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000 Midreshet Ben Gurion, Israel
| | - Satarupa Dey
- Department of Botany, Shyampur Siddheswari Mahavidyalaya, University of Calcutta, Ajodhya, Shyampur, Howrah, 711312 India
| | - Elza Bontempi
- Department of Mechanical and Industrial Engineering, INSTM Unit of Brescia, University of Brescia, Via Branze 38, 25123 Brescia, Italy
| | - Serena Ducoli
- Department of Mechanical and Industrial Engineering, INSTM Unit of Brescia, University of Brescia, Via Branze 38, 25123 Brescia, Italy
| | - A. Dick Vethaak
- Department of Environment and Health, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Institute for Risk Assessment Sciences, Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal 700073 India
| | - Stefania Federici
- Department of Mechanical and Industrial Engineering, INSTM Unit of Brescia, University of Brescia, Via Branze 38, 25123 Brescia, Italy
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15
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Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water. Microorganisms 2023; 11:microorganisms11020287. [PMID: 36838251 PMCID: PMC9960253 DOI: 10.3390/microorganisms11020287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.
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16
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Reineke W, Schlömann M. Microbial Communities: Structural and Functional Analyses with Classical Approach. Environ Microbiol 2023. [DOI: 10.1007/978-3-662-66547-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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17
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Virwani PD, Cai L, Yeung PKK, Qian G, Chen Y, Zhou L, Wong JWH, Wang Y, Ho JWK, Lau KK, Qian PY, Chung SK. Deficiency of exchange protein directly activated by cAMP (EPAC)-1 in mice augments glucose intolerance, inflammation, and gut dysbiosis associated with Western diet. MICROBIOME 2022; 10:187. [PMID: 36329549 PMCID: PMC9635209 DOI: 10.1186/s40168-022-01366-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Gut microbiota (GM) dysregulation, known as dysbiosis, has been proposed as a crucial driver of obesity associated with "Western" diet (WD) consumption. Gut dysbiosis is associated with increased gut permeability, inflammation, and insulin resistance. However, host metabolic pathways implicated in the pathophysiology of gut dysbiosis are still elusive. Exchange protein directly activated by cAMP (Epac) plays a critical role in cell-cell junction formation and insulin secretion. Here, we used homozygous Epac1-knockout (Epac1-/-), Epac2-knockout (Epac2-/-), and wild-type (WT) mice to investigate the role of Epac proteins in mediating gut dysbiosis, gut permeability, and inflammation after WD feeding. RESULTS The 16S rRNA gene sequencing of fecal DNA showed that the baseline GM of Epac2-/-, but not Epac1-/-, mice was represented by a significantly higher Firmicutes to Bacteroidetes ratio and significant alterations in several taxa compared to WT mice, suggesting that Epac2-/- mice had gut dysbiosis under physiological conditions. However, an 8-week WD led to a similar gut microbiome imbalance in mice regardless of genotype. While Epac1 deficiency modestly exacerbated the WD-induced GM dysbiosis, the WD-fed Epac2-/- mice had a more significant increase in gut permeability than corresponding WT mice. After WD feeding, Epac1-/-, but not Epac2-/-, mice had significantly higher mRNA levels of tumor necrosis factor-alpha (TNF-α) and F4/80 in the epididymal white adipose tissue (EWAT), increased circulating lipocalin-2 protein and more severe glucose intolerance, suggesting greater inflammation and insulin resistance in WD-fed Epac1-/- mice than corresponding WT mice. Consistently, Epac1 protein expression was significantly reduced in the EWAT of WD-fed WT and Epac2-/- mice. CONCLUSION Despite significantly dysregulated baseline GM and a more pronounced increase in gut permeability upon WD feeding, WD-fed Epac2-/- mice did not exhibit more severe inflammation and glucose intolerance than corresponding WT mice. These findings suggest that the role of gut dysbiosis in mediating WD-associated obesity may be context-dependent. On the contrary, we demonstrate that deficiency of host signaling protein, Epac1, drives inflammation and glucose intolerance which are the hallmarks of WD-induced obesity. Video abstract.
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Affiliation(s)
- Preeti Dinesh Virwani
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Lin Cai
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong S.A.R. China
| | - Patrick Ka Kit Yeung
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Gordon Qian
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong S.A.R., China
| | - Yingxian Chen
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Lei Zhou
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Jason Wing Hon Wong
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Yu Wang
- Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
| | - Joshua Wing Kei Ho
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong S.A.R., China
| | - Kui Kai Lau
- Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong S.A.R., China
| | - Pei-Yuan Qian
- Department of Ocean Science and Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong S.A.R. China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
| | - Sookja Kim Chung
- Faculty of Medicine; Faculty of Innovation Engineering, Macau University of Science and Technology, Macau Special Administrative Region (S.A.R.), China
- School of Biomedical Sciences, Li Ka Shing (LKS) Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau S.A.R., China
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18
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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19
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Li Y, Hua D, Xu H, Jin F, Zhao Y, Chen L, Zhao B, Rosendahl LA, Zhu Z. Energy recovery from high ash-containing sewage sludge: Focusing on performance evaluation of bio-fuel production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157083. [PMID: 35780877 DOI: 10.1016/j.scitotenv.2022.157083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/28/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Hydrothermal liquefaction (HTL) has shown great potential to convert sewage sludge (SS) with high moisture into bio-crude. However, the disposal and reutilization of hydrothermal liquefaction wastewater (HTLWW) is a critical issue. Anaerobic digestion (AD) is proven to be an alternative to treat organic wastewater. Therefore, energy recovery from high ash-containing SS was studied by integrating AD with HTL. The effect of temperature on HTL efficiency was investigated and then methane production from HTLWW was conducted by AD with organic loading increasing from 2 g COD/L to 6 g COD/L. Results showed that the maximum bio-crude yield of 23.5 % was obtained at 350 °C. Methane yield of 309.4 mL CH4/g CODremoved was achieved at 2 g COD/L with COD removal rate of 72.5 %. Meanwhile, the microbial structure and abundance showed great shifts resulting from the adaptation to complex compounds. JGI-000079-D21, Aminicenantales, and Bacteroidetes_ vadinHA17 predominated in the bacterial community. Due to the presence of the toxic substances in HTLWW, such as phenolic and nitrogenous heterocyclic compounds, there was a decrease in methane yield when the organic loading was higher than 4 g COD/L. The organic matters in extracellular polymeric substances (EPS) were rich in fulvic acid-like and humic acid-like substances due to the attack and stimulation of toxicants. Under the condition of unstable fermentation, Advenella and Bacillus first appeared as phenol and pyridine degrading bacteria, respectively. The microbial diversity declined sharply to demonstrate the toxic effect of the refractory organics existing at high organic loading. The enrichment of Methanosaeta in methanogens meant that acetotrophic metabolism is the dominant pathway in methanogenesis. In this study, the profile of bio-fuel production from high ash-containing SS would provide an integrated reference to treat wet biomass and recover energy simultaneously.
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Affiliation(s)
- Yan Li
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China.
| | - Dongliang Hua
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Haipeng Xu
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Fuqiang Jin
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Yuxiao Zhao
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Lei Chen
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Baofeng Zhao
- Energy Research Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Biomass Gasification Technology, Jinan 250014, China; School of Energy and Power Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China
| | - Lasse A Rosendahl
- Department of Energy Technology, Aalborg University, Aalborg 9220, Denmark
| | - Zhe Zhu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China.
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20
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Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data. Microorganisms 2022; 10:microorganisms10101961. [PMID: 36296237 PMCID: PMC9609705 DOI: 10.3390/microorganisms10101961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.
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21
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Rodrigues CJC, de Carvalho CCCR. Cultivating marine bacteria under laboratory conditions: Overcoming the “unculturable” dogma. Front Bioeng Biotechnol 2022; 10:964589. [PMID: 36061424 PMCID: PMC9428589 DOI: 10.3389/fbioe.2022.964589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.
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Affiliation(s)
- Carlos J. C. Rodrigues
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory I4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory I4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- *Correspondence: Carla C. C. R. de Carvalho,
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22
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Nanopore metatranscriptomics reveals cryptic catfish species as potential Shigella flexneri vectors in Kenya. Sci Rep 2022; 12:13875. [PMID: 35974032 PMCID: PMC9380665 DOI: 10.1038/s41598-022-17036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022] Open
Abstract
Bacteria in the Shigella genus remain a major cause of dysentery in sub-Saharan Africa, and annually cause an estimated 600,000 deaths worldwide. Being spread by contaminated food and water, this study highlights how wild caught food, in the form of freshwater catfish, can act as vectors for Shigella flexneri in Southern Kenya. A metatranscriptomic approach was used to identify the presence of Shigella flexneri in the catfish which had been caught for consumption from the Galana river. The use of nanopore sequencing was shown to be a simple and effective method to highlight the presence of Shigella flexneri and could represent a potential new tool in the detection and prevention of this deadly pathogen. Rather than the presence/absence results of more traditional testing methods, the use of metatranscriptomics highlighted how primarily one SOS response gene was being transcribed, suggesting the bacteria may be dormant in the catfish. Additionally, COI sequencing of the vector catfish revealed they likely represent a cryptic species. Morphological assignment suggested the fish were widehead catfish Clarotes laticeps, which range across Africa, but the COI sequences from the Kenyan fish are distinctly different from C. laticeps sequenced in West Africa.
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23
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Quintanilla-Mena MA, Olvera-Novoa MA, Sánchez-Tapia IA, Lara-Pérez LA, Rivas-Reyes I, Gullian-Klanian M, Patiño-Suárez MV, Puch-Hau CA. The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota. Arch Microbiol 2022; 204:463. [PMID: 35792945 DOI: 10.1007/s00203-022-03080-9] [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: 08/26/2021] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022]
Abstract
For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.
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Affiliation(s)
- Mercedes A Quintanilla-Mena
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Miguel A Olvera-Novoa
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Itzel A Sánchez-Tapia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Luis A Lara-Pérez
- Tecnológico Nacional de México Campus Instituto Tecnológico de la Zona Maya, Carretera Chetumal-Escárcega km 21.5, C.P. 77965, Ejido Juan Sarabia, Quintana Roo, Mexico
| | - Isajav Rivas-Reyes
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Mariel Gullian-Klanian
- Universidad Marista de Mérida, Periférico Norte Tablaje Catastral 13941, Carretera Mérida-Progreso, P.O. Box 97300, Mérida, Yucatán, Mexico
| | - María V Patiño-Suárez
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico
| | - Carlos A Puch-Hau
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Departamento de Recursos de Mar, Unidad Mérida, Km. 6 Antigua Carretera a Progreso, Apdo. Postal 73-CORDEMEX, 97310, Mérida, Yucatán, Mexico.
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24
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Adenaike AS, Akpan U, Awopejo OO, Oloye OS, Alli-Balogun AO, Agbaje M, Ikeobi CON. Characterization of the cecal microbiome composition of Nigerian indigenous chickens. Trop Anim Health Prod 2022; 54:211. [PMID: 35687206 DOI: 10.1007/s11250-022-03191-x] [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: 02/21/2022] [Accepted: 04/30/2022] [Indexed: 02/07/2023]
Abstract
Poultry cecum microbes are dynamic and complex. They play important roles in disease prevention, detoxification of harmful substances, nutrient processing, and ingestion harvesting. It may be possible to increase poultry productivity by better understanding and controlling the microbial population. We analyzed the composition and function of Nigerian hens' cecal microbiota using high-throughput sequencing methods. Using high-throughput sequencing of the 16S rRNA genes (V1-V9) hypervariable regions, the cecal microbiota of three Nigerian indigenous chicken genotypes (Naked neck, Frizzle, and Normal feather) was described and compared. A total of two phyla were represented among the three genotypes (Firmicutes and Proteobacteria). Microbiological diversity was found in the community, with naked neck having the most evenness, followed by normal feather, which had the least. There were a lot of similarities between the naked neck and frizzle feather chicken groups when it came to genetic diversity between them. For example, the bacterial cecal microbiota of the naked neck chickens was more diverse, with a higher concentration of motility proteins, two-component systems, bacterial secretion systems, and the formation and breakdown of secondary metabolites. More understanding on gut microbiota roles and interactions will help Nigerian poultry farmers improve their methods and give valuable data for the study of bacteria in the chicken gut.
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Affiliation(s)
- A S Adenaike
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria.
| | - U Akpan
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - O O Awopejo
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - O S Oloye
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - A O Alli-Balogun
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
| | - M Agbaje
- Department of Veterinary Microbiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - C O N Ikeobi
- Department of Animal Breeding and Genetics, Federal University of Agriculture, P.M.B 2240, Alabata Road, Abeokuta, Ogun, Nigeria
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25
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Bowers RM, Nayfach S, Schulz F, Jungbluth SP, Ruhl IA, Sheremet A, Lee J, Goudeau D, Eloe-Fadrosh EA, Stepanauskas R, Malmstrom RR, Kyrpides NC, Dunfield PF, Woyke T. Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution. THE ISME JOURNAL 2022; 16:1337-1347. [PMID: 34969995 PMCID: PMC9039060 DOI: 10.1038/s41396-021-01178-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.
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Affiliation(s)
- Robert M. Bowers
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Stephen Nayfach
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Frederik Schulz
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Sean P. Jungbluth
- grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Ilona A. Ruhl
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada ,grid.419357.d0000 0001 2199 3636National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Andriy Sheremet
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada
| | - Janey Lee
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Danielle Goudeau
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Emiley A. Eloe-Fadrosh
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Ramunas Stepanauskas
- grid.296275.d0000 0000 9516 4913Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME USA
| | - Rex R. Malmstrom
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Nikos C. Kyrpides
- grid.451309.a0000 0004 0449 479XU.S. Department of Energy, Joint Genome Institute, Berkeley, CA USA
| | - Peter F. Dunfield
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada
| | - Tanja Woyke
- U.S. Department of Energy, Joint Genome Institute, Berkeley, CA, USA.
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26
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Newton K, Gonzalez E, Pitre FE, Brereton NJB. Microbial community origin and fate through a rural wastewater treatment plant. Environ Microbiol 2022; 24:2516-2542. [PMID: 35466495 DOI: 10.1111/1462-2920.16025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/20/2022] [Indexed: 11/29/2022]
Abstract
Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post-treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kymberly Newton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
| | - Emmanuel Gonzalez
- Canadian Center for Computational Genomics, Department of Human Genetics, McGill University, Montréal, H3A 1A4, Canada
| | - Frederic E Pitre
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
| | - Nicholas J B Brereton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, H1X 2B2, Canada
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27
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Deng C, Zhao R, Qiu Z, Li B, Zhang T, Guo F, Mu R, Wu Y, Qiao X, Zhang L, Cheng JJ, Ni J, Yu K. Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151635. [PMID: 34774959 DOI: 10.1016/j.scitotenv.2021.151635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Landfills are important sources of microorganisms associated with anaerobic digestion. However, the knowledge on microbiota along with their functional potential in this special habitat are still lacking. In this study, we recovered 1168 non-redundant metagenome-assembled genomes (MAGs) from nine landfill leachate samples collected from eight cities across China, spanning 42 phyla, 73 classes, 114 orders, 189 families, and 267 genera. Totally, 74.1% of 1168 MAGs could not be classified to any known species and 5.9% of these MAGs belonged to microbial dark matter phyla. Two putative novel classes were discovered from landfill leachate samples. The identification of thousands of novel carbohydrate-active enzymes showed similar richness level compared to the cow rumen microbiota. The methylotrophic methanogenic pathway was speculated to contribute significantly to methane production in the landfill leachate because of its co-occurrence with the acetoclastic and hydrogenotrophic methanogenic pathways. The genetic potential of dissimilatory nitrate reduction to ammonium (DNRA) was observed, implying DNRA may play a role in ammonium generation in landfill leachate. These findings implied that landfill leachate might be a valuable microbial resource repository and filled the previous understanding gaps for both methanogenesis and nitrogen cycling in landfill leachate microbiota. Our study provides a comprehensive genomic catalog and substantially provides unprecedented taxonomic and functional profiles of the landfill leachate microbiota.
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Affiliation(s)
- Chunfang Deng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Feng Guo
- School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Rong Mu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yang Wu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xuejiao Qiao
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Liyu Zhang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jay J Cheng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Biological & Agricultural Engineering Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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Mahnkopp-Dirks F, Radl V, Kublik S, Gschwendtner S, Schloter M, Winkelmann T. Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease. Front Microbiol 2022; 13:841558. [PMID: 35401446 PMCID: PMC8993231 DOI: 10.3389/fmicb.2022.841558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/14/2022] [Indexed: 01/04/2023] Open
Abstract
Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.
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Affiliation(s)
- Felix Mahnkopp-Dirks
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
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Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng). Arch Microbiol 2022; 204:208. [PMID: 35275265 DOI: 10.1007/s00203-022-02815-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023]
Abstract
Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.
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Pawar MM, Shivanna B, Prasannakumar MK, Parivallal PB, Suresh K, Meenakshi NH. Spatial distribution and community structure of microbiota associated with cowpea aphid ( Aphis craccivora Koch). 3 Biotech 2022; 12:75. [PMID: 35251878 PMCID: PMC8861231 DOI: 10.1007/s13205-022-03142-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/07/2022] [Indexed: 01/01/2023] Open
Abstract
Aphid populations were collected on cowpea, dolichos, redgram and black gram from Belagavi and Udupi locations. The samples were shotgun sequenced using the Illumina NovaSeq 6000 system to understand the spatial distribution and community structure of microbiota (especially bacteria) associated with aphids. In the present study, we identified obligatory nutritional symbiont Buchnera aphidicola and facultative symbionts Rickettsia sp. and Bacteroidetes endosymbiont of Geopemphigus sp. in all the aphid samples studied, although in varied abundance. On the other hand, Serratia symbiotica, Arsenophonus sp. and Acinetobacter sp. were only found in aphids on specific host plants, suggesting that host plants might influence the bacterial community structure. Furthermore, our study revealed that microbiota other than bacteria were highly insignificant in the aphid populations. Additionally, functional annotation of aphid metagenomes identified several pathways and enzymes involved in various physiological and ecological functions. Amino acid and vitamin biosynthesis-related pathways were predominant than carbohydrate metabolism, owing to their feeding habit and nutritional requirement. Chaperones related to stress tolerance such as GroEL and DnaK were identified. Enzymes involved in toxic chemical metabolisms such as glutathione transferase, phosphodiesterases and ABC transferases were observed. These enzymes may confer resistance to pesticides in the aphid populations. Overall, our results support the importance of host plants in structuring bacterial communities in aphids and show the functional roles of symbionts in aphid survival and development. Thus, these findings can be the basis for further detailed investigations and devising better strategies to manage the pests in field conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03142-1.
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Affiliation(s)
- Madhusudan M. Pawar
- grid.413008.e0000 0004 1765 8271Insect Molecular Biology Laboratory, Department of Agricultural Entomology, University of Agricultural Sciences, Bangalore, 560065 India
| | - B. Shivanna
- grid.413008.e0000 0004 1765 8271Insect Molecular Biology Laboratory, Department of Agricultural Entomology, University of Agricultural Sciences, Bangalore, 560065 India
| | - M. K. Prasannakumar
- grid.413008.e0000 0004 1765 8271Plant PathoGenOmic Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bangalore, 560065 India
| | - P. Buela Parivallal
- grid.413008.e0000 0004 1765 8271Plant PathoGenOmic Laboratory, Department of Plant Pathology, University of Agricultural Sciences, Bangalore, 560065 India
| | - Kiran Suresh
- grid.10388.320000 0001 2240 3300Department of Ecophysiology, University of Bonn, 53115 Bonn, Germany
| | - N. H. Meenakshi
- grid.413008.e0000 0004 1765 8271Insect Molecular Biology Laboratory, Department of Agricultural Entomology, University of Agricultural Sciences, Bangalore, 560065 India
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Belman S, Chaguza C, Kumar N, Lo S, Bentley SD. A new perspective on ancient Mitis group streptococcal genetics. Microb Genom 2022; 8. [PMID: 35225216 PMCID: PMC8942026 DOI: 10.1099/mgen.0.000753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mitis group Streptococcus are human obligate bacteria residing in the nasopharynx and oral cavity. They comprise both commensal and pathogenic species with the most well-known being Streptococcus pneumoniae – a leading cause of meningitis and pneumonia. A primary difference between the commensal and pathogenic species is the presence of the polysaccharide capsule – a major virulence factor in S. pneumoniae, also present in other commensal species. Our current understanding of the evolutionary divergence of the pathogenic and commensal species has been inferred from extant strains. Ancient genomes can further elucidate streptococcal evolutionary history. We extracted streptococcal genome reads from a 5700-year-old ancient metagenome and worked towards characterizing them. Due to excessive within- and between-species recombination common among streptococci we were unable to parse individual species. Further, the composite reads of the ancient metagenome do not fit within the diversity of any specific extant species. Using a capsular gene database and AT-content analysis we determined that this ancient metagenome is missing polysaccharide synthesis genes integral to streptococcal capsule formation. The presence of multiple zinc metalloproteases suggests that adaptation to host IgA1 had begun and the presence of other virulence factors further implies development of close host–microbe interactions, though the absence of a capsule suggests an inability to cause invasive disease. The presence of specific virulence factors such as pneumolysin implies stable maintenance of such genes through streptococcal evolution that may strengthen their value as anti-pneumococcal vaccine antigens, while maintaining awareness of their potential presence in commensal species. Following from Jensen et al.’s initial analysis we provide historical context for this long time human nasopharyngeal resident, the Mitis group Streptococcus.
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Affiliation(s)
- Sophie Belman
- Department of Genetics, University of Cambridge, Cambridge, UK
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Chrispin Chaguza
- Yale School of Medicine, New Haven, CT, USA
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie Lo
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
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Ben Khedher M, Ghedira K, Rolain JM, Ruimy R, Croce O. Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies. Int J Mol Sci 2022; 23:1395. [PMID: 35163319 PMCID: PMC8835973 DOI: 10.3390/ijms23031395] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Since then, these technologies have continued to evolve, and recently, long-read sequencing has overcome previous limitations in terms of accuracy, thus expanding its applications in genomics, transcriptomics and metagenomics. In this review, we describe a brief history of the bacterial genome sequencing revolution and its application in public health and molecular epidemiology. We present a chronology that encompasses the various technological developments: whole-genome shotgun sequencing, high-throughput sequencing, long-read sequencing. We mainly discuss the application of next-generation sequencing to decipher bacterial genomes. Secondly, we highlight how long-read sequencing technologies go beyond the limitations of traditional short-read sequencing. We intend to provide a description of the guiding principles of the 3rd generation sequencing applications and ongoing improvements in the field of microbial medical research.
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Affiliation(s)
- Mariem Ben Khedher
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis 1002, Tunisia;
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, 13005 Marseille, France;
| | - Raymond Ruimy
- Bacteriology Laboratory, Archet 2 Hospital, CHU Nice, 06000 Nice, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM, Université Côte D’Azur, 06108 Nice, France
| | - Olivier Croce
- Institute for Research on Cancer and Aging Nice (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06108 Nice, France
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Bonomo MG, Calabrone L, Scrano L, Bufo SA, Di Tomaso K, Buongarzone E, Salzano G. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:48. [PMID: 34978609 PMCID: PMC8724107 DOI: 10.1007/s10661-021-09637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/20/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.
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Affiliation(s)
| | - Luana Calabrone
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European Cultures, University of Basilicata, Potenza, Italy
| | - Sabino Aurelio Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Katia Di Tomaso
- Department of Sciences, University of Basilicata, Potenza, Italy
| | | | - Giovanni Salzano
- Department of Sciences, University of Basilicata, Potenza, Italy
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Tran KM, Lee HM, Thai TD, Shen J, Eyun SI, Na D. Synthetically engineered microbial scavengers for enhanced bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126516. [PMID: 34218189 DOI: 10.1016/j.jhazmat.2021.126516] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.
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Affiliation(s)
- Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.
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Sanjaya RE, Putri KDA, Kurniati A, Rohman A, Puspaningsih NNT. In silico characterization of the GH5-cellulase family from uncultured microorganisms: physicochemical and structural studies. J Genet Eng Biotechnol 2021; 19:143. [PMID: 34591195 PMCID: PMC8484414 DOI: 10.1186/s43141-021-00236-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Hydrolysis of cellulose-based biomass by cellulases produce fermented sugar for making biofuels, such as bioethanol. Cellulases hydrolyze the β-1,4-glycosidic linkage of cellulose and can be obtained from cultured and uncultured microorganisms. Uncultured microorganisms are a source for exploring novel cellulase genes through the metagenomic approach. Metagenomics concerns the extraction, cloning, and analysis of the entire genetic complement of a habitat without cultivating microbes. The glycoside hydrolase 5 family (GH5) is a cellulase family, as the largest group of glycoside hydrolases. Numerous variants of GH5-cellulase family have been identified through the metagenomic approach, including CelGH5 in this study. University-CoE-Research Center for Biomolecule Engineering, Universitas Airlangga successfully isolated CelGH5 from waste decomposition of oil palm empty fruit bunches (OPEFB) soil by metagenomics approach. The properties and structural characteristics of GH5-cellulases from uncultured microorganisms can be studied using computational tools and software. RESULTS The GH5-cellulase family from uncultured microorganisms was characterized using standard computational-based tools. The amino acid sequences and 3D-protein structures were retrieved from the GenBank Database and Protein Data Bank. The physicochemical analysis revealed the sequence length was roughly 332-751 amino acids, with the molecular weight range around 37-83 kDa, dominantly negative charges with pI values below 7. Alanine was the most abundant amino acid making up the GH5-cellulase family and the percentage of hydrophobic amino acids was more than hydrophilic. Interestingly, ten endopeptidases with the highest average number of cleavage sites were found. Another uniqueness demonstrated that there was also a difference in stability between in silico and wet lab. The II values indicated CelGH5 and ACA61162.1 as unstable enzymes, while the wet lab showed they were stable at broad pH range. The program of SOPMA, PDBsum, ProSA, and SAVES provided the secondary and tertiary structure analysis. The predominant secondary structure was the random coil, and tertiary structure has fulfilled the structure quality of QMEAN4, ERRAT, Ramachandran plot, and Z score. CONCLUSION This study can afford the new insights about the physicochemical and structural properties of the GH5-cellulase family from uncultured microorganisms. Furthermore, in silico analysis could be valuable in selecting a highly efficient cellulases for enhanced enzyme production.
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Affiliation(s)
- Rahmat Eko Sanjaya
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Chemistry Education Study Program, Faculty of Teacher Training and Education, Universitas Lambung Mangkurat, Jl. Brigjend. H. Hasan Basry, Banjarmasin, Kalimantan, 70123, Indonesia
| | - Kartika Dwi Asni Putri
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Anita Kurniati
- Mathematics and Natural Science Study Program, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Health, Faculty of Vocational Studies, Kampus B Universitas Airlangga, Surabaya, East Java, 60286, Indonesia
| | - Ali Rohman
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- University-CoE-Research Centre for Bio-Molecule Engineering, 2nd Floor ITD Building, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
- Department of Chemistry, Faculty of Science and Technology, Kampus C Universitas Airlangga, Mulyorejo, Surabaya, East Java, 60115, Indonesia.
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Seasonal Characterization of the Endophytic Fungal Microbiome of Mulberry ( Morus spp.) Cultivars Resistant and Susceptible to Sclerotiniosis. Microorganisms 2021; 9:microorganisms9102052. [PMID: 34683372 PMCID: PMC8537754 DOI: 10.3390/microorganisms9102052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 01/05/2023] Open
Abstract
The endophytic microbiome is thought to play an important role in promoting plant growth and health. Using culture-independent and culture-dependent protocols, this study characterized the seasonal shifts in the endophytic fungal microbiota of four mulberry (Morus L.) cultivars having different levels of resistance to mulberry fruit sclerotiniosis. Core endophytes can be obtained by two approaches, and they were divided into two clusters by season. Spring samples harbored higher operational taxonomic units (OTUs) and α-diversity, while autumn samples had more sequences or isolates of the fungal class Dothideomycetes with the representative orders Capnodiales and Pleosporales. While comparing different mulberry cultivars, we found that the total number of OTUs in susceptible cultivars was higher than that of resistant cultivars, and Cladosporium sp. were observed in all. Notably, the causal agent of fruit sclerotiniosis (Scleromitrula shiraiana) was only detected in susceptible cultivars. Collectively, our work elucidated significant variations in the mulberry endophytic microbiome, mainly because of seasonal shifts, and the fact that the host cultivars and mulberry endophytic fungal community appeared to have a certain connection with the resistance level of mulberry fruit to sclerotiniosis. These results provided valuable information on the isolation and culturing of mulberry endophytes that could be applied to improve mulberry fruit production and health.
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Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies. mSystems 2021; 6:e0075021. [PMID: 34427527 PMCID: PMC8407471 DOI: 10.1128/msystems.00750-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The advent of high-throughput sequencing techniques has recently provided an astonishing insight into the composition and function of the human microbiome. Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. Despite the wide availability and the enormous potential for clinical and translational applications, ONT is poorly standardized in terms of sampling and storage conditions, DNA extraction, library creation, and bioinformatic classification. Here, we present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatic evaluation for complex microbiomes sequenced with ONT. Our findings from buccal and rectal swabs and DNA extraction experiments indicate that methods that were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Our benchmarking experiments reveal thresholds for analysis parameters that achieved excellent precision, recall, and area under the precision recall values and is superior to existing classifiers (Kraken2, Kaiju, and MetaMaps). Hence, our workflow provides an experimental and bioinformatic pipeline to perform a highly accurate analysis of complex microbial structures from buccal and rectal swabs. IMPORTANCE Advanced microbiome analysis relies on sequencing of short DNA fragments from microorganisms like bacteria, fungi, and viruses. More recently, long fragment DNA sequencing of 3rd generation sequencing has gained increasing importance and can be rapidly conducted within a few hours due to its potential real-time sequencing. However, the analysis and correct identification of the microbiome relies on a multitude of factors, such as the method of sampling, DNA extraction, sequencing, and bioinformatic analysis. Scientists have used different protocols in the past that do not allow us to compare results across different studies and research fields. Here, we provide a comprehensive workflow from DNA extraction, sequencing, and bioinformatic workflow that allows rapid and accurate analysis of human buccal and rectal swabs with reproducible protocols. This workflow can be readily applied by many scientists from various research fields that aim to use long-fragment microbiome sequencing.
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Lonsdorf EV, Travis DA, Raphael J, Kamenya S, Lipende I, Mwacha D, Collins DA, Wilson M, Mjungu D, Murray C, Bakuza J, Wolf TM, Parsons MB, Deere JR, Lantz E, Kinsel MJ, Santymire R, Pintea L, Terio KA, Hahn BH, Pusey AE, Goodall J, Gillespie TR. The Gombe Ecosystem Health Project: 16 years of program evolution and lessons learned. Am J Primatol 2021; 84:e23300. [PMID: 34223656 PMCID: PMC8727649 DOI: 10.1002/ajp.23300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 12/30/2022]
Abstract
Infectious disease outbreaks pose a significant threat to the conservation of chimpanzees (Pan troglodytes) and all threatened nonhuman primates. Characterizing and mitigating these threats to support the sustainability and welfare of wild populations is of the highest priority. In an attempt to understand and mitigate the risk of disease for the chimpanzees of Gombe National Park, Tanzania, we initiated a long-term health-monitoring program in 2004. While the initial focus was to expand the ongoing behavioral research on chimpanzees to include standardized data on clinical signs of health, it soon became evident that the scope of the project would ideally include diagnostic surveillance of pathogens for all primates (including people) and domestic animals, both within and surrounding the National Park. Integration of these data, along with in-depth post-mortem examinations, have allowed us to establish baseline health indicators to inform outbreak response. Here, we describe the development and expansion of the Gombe Ecosystem Health project, review major findings from the research and summarize the challenges and lessons learned over the past 16 years. We also highlight future directions and present the opportunities and challenges that remain when implementing studies of ecosystem health in a complex, multispecies environment.
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Affiliation(s)
- Elizabeth V Lonsdorf
- Department of Psychology and Biological Foundations of Behavior Program, Franklin & Marshall College, Lancaster, Pennsylvania, USA
| | - Dominic A Travis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Jane Raphael
- Gombe National Park, Tanzania Nationals Park, Kigoma, Tanzania
| | - Shadrack Kamenya
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - Iddi Lipende
- Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - D Anthony Collins
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - Michael Wilson
- Departments of Anthropology and Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Deus Mjungu
- Gombe Stream Research Center, The Jane Goodall Institute, Kigoma, Tanzania
| | - Carson Murray
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, District of Columbia, USA
| | - Jared Bakuza
- College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Tiffany M Wolf
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Michele B Parsons
- Division of Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica R Deere
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Emma Lantz
- California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Michael J Kinsel
- Zoological Pathology Program, University of Illinois, Brookfield, Illinois, USA
| | - Rachel Santymire
- Davee Center for Epidemiology and Endocrinology, Lincoln Park Zoo, Chicago, Illinois, USA
| | | | - Karen A Terio
- Zoological Pathology Program, University of Illinois, Brookfield, Illinois, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Jane Goodall
- The Jane Goodall Institute, Vienna, Virginia, USA
| | - Thomas R Gillespie
- Departments of Environmental Sciences and Environmental Health and Program in Population Biology, Emory University, Atlanta, Georgia, USA
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De Zutter N, Ameye M, Debode J, De Tender C, Ommeslag S, Verwaeren J, Vermeir P, Audenaert K, De Gelder L. Shifts in the rhizobiome during consecutive in planta enrichment for phosphate-solubilizing bacteria differentially affect maize P status. Microb Biotechnol 2021; 14:1594-1612. [PMID: 34021699 PMCID: PMC8313256 DOI: 10.1111/1751-7915.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate-solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P-solubilization and rhizosphere competence. We used an ecologically relevant combination of iron- and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants' P statuses, non-destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize's P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth-promoting and P-solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.
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Affiliation(s)
- Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Jane Debode
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Caroline De Tender
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
- Department of Applied Mathematics, Computer Science and StatisticsGhent UniversityKrijgslaan 281 S9GhentB‐9000Belgium
| | - Sarah Ommeslag
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Jan Verwaeren
- Research Unit Knowledge‐based Systems (KERMIT)Department of Data Analysis and Mathematical ModelingGhent UniversityCoupure links 653GhentB‐9000Belgium
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA)Faculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Leen De Gelder
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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Mishra S, Goyal D, Phurailatpam L. Targeted 16S rRNA gene and ITS2 amplicon sequencing of leaf and spike tissues of Piper longum identifies new candidates for bioprospecting of bioactive compounds. Arch Microbiol 2021; 203:3851-3867. [PMID: 34013420 DOI: 10.1007/s00203-021-02356-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022]
Abstract
Piper longum (also known as Indian long pepper) is widely used in Ayurvedic, Siddha and Unani medicine systems. The principle bioactive compound of this plant is piperine, which mainly accumulates in the fruits called spikes. The report of piperine production by endophytic microbes isolated from Piper sp., motivated us to investigate the endophytic microbial diversity associated with the spikes vis-à-vis leaves (which contain negligible levels of piperine). This is the first report to use metagenomics approach to unravel the endophytic microbial diversity in P. longum. Our results indicate that 2, 56, 631 bacterial OTUs and 1090 fungal OTUs were picked cumulatively from both the tissues. Although bacterial and fungal endophytes occupy the same niche, remarkable differences exist in their diversity and abundance. For instance, the most abundant bacterial genera in spikes were Nocardioides and Pseudonocardia (Phylum Actinobacteria; reported to produce bioactive compounds); while, in leaves were Larkinella and Hymenobacter (Phylum Bacteriodetes). Likewise, the fungal endophytes, Periconia, Cladosporium and Coniothyrium (which have been earlier reported to produce commercially important metabolites including piperine), were also present in high abundance in spikes, in comparison to leaves. Further, the results of PICRUSt analysis reveal the high metabolic potential of spike-associated bacteria for secondary metabolism, namely biosynthesis of alkaloids (including pyridine/piperidine), terpenes, flavonoids and antibiotics. Therefore, our findings indicate that the endophytes abundant or unique in spikes could be explored for bioprospecting of novel/commercially important metabolites; an approach that has both ecological and economical benefits.
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Affiliation(s)
- Sushma Mishra
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, India.
| | - Deepika Goyal
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, India
| | - Laccy Phurailatpam
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed-to-be-University), Agra, Uttar Pradesh, India
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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Rai A, Bhattacharjee A. Molecular profiling of microbial community structure and their CAZymes via metagenomics, from Tsomgo lake in the Eastern Himalayas. Arch Microbiol 2021; 203:3135-3146. [PMID: 33813595 DOI: 10.1007/s00203-021-02278-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
The present study is the first of its kind which is focused on Tsomgo lake, a high-altitude lake, located in the Eastern Himalayas of Sikkim. To get a major insight into the bacterial diversity, the shotgun sequencing was carried out in Illumina platform. Our results showed that both the samples TLSS1 (soil) and TLSW1 (water), had Proteobacteria as the most abundant taxa. Cluster of Orthologous group (COG) functional category of TLSS1 has 1,46,965 predicted functions. Cluster of Orthologous Group (COG) functional category of TLSW1 has 1,34,773 predicted functions. Kyoto Encyclopedia of Gene and Genomes (KEGG) functional category of TLSS1 has 1,76,825 predicted functions, most of the sequence fall in metabolism followed by Environmental information processing function. (KEGG) functional category of TLSW1 has 1,62,696 predicted functions and it follows the same pattern as TLSS1. Our studies also provide insight into the presence of distribution of different carbohydrate-active enzymes (CAZymes) present in Tsomgo lake. We have found that in case of both the samples TLSW1 and TLSS1, GlycosylTransferases were active followed by GlycosylHydrolase. The result found, represents for the first time very important findings related to the microbial diversity and the abundance of CAZymes in Tsomgo lake one of the pristine high-altitude lakes in Sikkim.
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Affiliation(s)
- Aditi Rai
- Department of Microbiology, University of North Bengal, Darjeeling, 734013, West Bengal, India
| | - Arindam Bhattacharjee
- Department of Microbiology, University of North Bengal, Darjeeling, 734013, West Bengal, India.
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45
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Guo H, Gibson SA, Ting JPY. Gut microbiota, NLR proteins, and intestinal homeostasis. J Exp Med 2021; 217:152098. [PMID: 32941596 PMCID: PMC7537383 DOI: 10.1084/jem.20181832] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
The gastrointestinal tract harbors a highly complex microbial community, which is referred to as gut microbiota. With increasing evidence suggesting that the imbalance of gut microbiota plays a significant role in the pathogenesis of multiple diseases, interactions between the host immune system and the gut microbiota are now attracting emerging interest. Nucleotide-binding and leucine-rich repeat–containing receptors (NLRs) encompass a large number of innate immune sensors and receptors, which mediate the activation of Caspase-1 and the subsequent release of mature interleukin-1β and interleukin-18. Several family members have been found to restrain rather than activate inflammatory cytokines and immune signaling. NLR family members are central regulators of pathogen recognition, host immunity, and inflammation with utmost importance in human diseases. In this review, we focus on the potential roles played by NLRs in controlling and shaping the microbiota community and discuss how the functional axes interconnecting gut microbiota with NLRs impact the modulation of colitis, inflammatory bowel diseases, and colorectal cancer.
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Affiliation(s)
- Hao Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara A Gibson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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46
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Rasmussen TS, Streidl T, Hitch TCA, Wortmann E, Deptula P, Kofoed MVW, Riedel T, Neumann-Schaal M, Hansen M, Nielsen DS, Clavel T, Vogensen FK. Sporofaciens musculi gen. nov., sp. nov., a novel bacterium isolated from the caecum of an obese mouse. Int J Syst Evol Microbiol 2021; 71. [PMID: 33512312 DOI: 10.1099/ijsem.0.004673] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A bacterial strain, designated WCA-9-b2T, was isolated from the caecal content of an 18-week-old obese C57BL/6NTac male mouse. According to phenotypic analyses, the isolate was rod-shaped, strictly anaerobic, spore-forming, non-motile and Gram-stain-positive, under the conditions tested. Colonies were irregular and non-pigmented. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the order Clostridiales with Dorea longicatena ATCC 27755T (94.9 % sequence identity), Ruminococcus gnavus ATCC 29149T (94.8%) and Clostridium scindens ATCC 35704T (94.3%) being the closest relatives. Whole genome sequencing showed an average nucleotide identity <74.23 %, average amino acid identity <64.52-74.67 % and percentage of conserved proteins values <50 % against the nine closest relatives (D. longicatena, Ruminococcus gnavus, C. scindens, Dorea formicigenerans, Ruminococcus lactaris, Clostridium hylemonae, Merdimonas faecis, Faecalicatena contorta and Faecalicatena fissicatena). The genome-based G+C content of genomic DNA was 44.4 mol%. The major cellular fatty acids were C16 : 0 (24.5%), C18 : 1 cis9 (19.8 %), C16 : 0 DMA (11.7%), C18 : 0 (8.4%) and C14 : 0 (6.6%). Respiratory quinones were not detected. The predominant metabolic end products of glucose fermentation were acetate and succinate. Production of CO2 and H2 were detected. Based on these data, we propose that strain WCA-9-b2T represents a novel species within a novel genus, for which the name Sporofaciens musculi gen. nov., sp. nov. is proposed. The type strain is WCA-9-b2T (=DSM 106039T=CECT 30156T).
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Theresa Streidl
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Esther Wortmann
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Paulina Deptula
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Michael V W Kofoed
- Microbial Conversion Technologies Research Group, Section for Biological and Chemical Engineering, Department of Engineering, Aarhus University, Aarhus, Denmark
| | - Thomas Riedel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Hansen
- Center for Advanced Bioimaging, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas Clavel
- ZIEL Core Facility Microbiome, Technical University of Munich, Freising, Germany.,Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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47
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Jeong J, Yun K, Mun S, Chung WH, Choi SY, Nam YD, Lim MY, Hong CP, Park C, Ahn YJ, Han K. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep 2021; 11:1727. [PMID: 33462291 PMCID: PMC7814050 DOI: 10.1038/s41598-020-80826-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
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Affiliation(s)
- Jinuk Jeong
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyeongeui Yun
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Song-Yi Choi
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Young-do Nam
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Chang Pyo Hong
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - ChanHyeok Park
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Yong Ju Ahn
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea.
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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48
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Thompson TW, Geornaras I, Delmore RJ, McFarlane BJ, Belk KE, Nair MN. Investigating the Etiology of Sour Knuckles in Postchilled Beef Carcasses. MEAT AND MUSCLE BIOLOGY 2020. [DOI: 10.22175/mmb.11557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Development of sourness in beef round muscle cuts, such as knuckles, has been a long-standing issue in the beef industry with little characterization. Therefore, the objective of this study was to investigate and characterize the sour odor associated with beef knuckles using sensory, analytical (gas chromatography-mass spectrometry [GC-MS]), and microbiological approaches. Knuckles (n = 10) with no sour odor (control), a slight sour odor, or severe sour odor were collected during fabrication from a commercial beef processing plant. In addition, the synovial fluid from the femur joint, and the femur surface associated with the collected knuckles, were sponge-sampled. Knuckles were separated into 2 halves, with one half subjected to an odor panel, GC-MS, and microbial analyses on the day of collection (day 0). The remaining half was analyzed for odor and microbial populations following 35 d of vacuum-packaged storage at 0°C ± 2°C (day 35). Odor panelists identified differences (P < 0.05) between control and sour knuckles (slight sour odor and severe sour odor) for all attributes tested (off-odor, oxidation, putrid, and sour notes) regardless of storage day. GC-MS analysis found no statistical difference (P > 0.05) in volatiles between control and severe-sour-odor samples. Microbial analysis (aerobic plate counts and lactic acid bacteria counts) of muscle tissue on day 0 and day 35 of storage revealed no (P > 0.05) differences between the 3 treatment groups. Similarly, no (P > 0.05) differences between the treatment groups were obtained following analysis of synovial fluid and femur surface sponge samples for psychrotrophic anaerobic sporeformer counts. The findings of the study indicated that the souring condition in knuckles exists at identifiable intensities with no volatile acid or microbial population differences; therefore, further investigation is needed to determine the etiology.
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Affiliation(s)
| | | | | | | | - Keith E. Belk
- Colorado State University Department of Animal Sciences
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Eberhardt MF, Irazoqui JM, Amadio AF. β-Galactosidases from a Sequence-Based Metagenome: Cloning, Expression, Purification and Characterization. Microorganisms 2020; 9:microorganisms9010055. [PMID: 33379234 PMCID: PMC7823827 DOI: 10.3390/microorganisms9010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/24/2022] Open
Abstract
Stabilization ponds are a common treatment technology for wastewater generated by dairy industries. Large proportions of cheese whey are thrown into these ponds, creating an environmental problem because of the large volume produced and the high biological and chemical oxygen demands. Due to its composition, mainly lactose and proteins, it can be considered as a raw material for value-added products, through physicochemical or enzymatic treatments. β-Galactosidases (EC 3.2.1.23) are lactose modifying enzymes that can transform lactose in free monomers, glucose and galactose, or galactooligosacharides. Here, the identification of novel genes encoding β-galactosidases, identified via whole-genome shotgun sequencing of the metagenome of dairy industries stabilization ponds is reported. The genes were selected based on the conservation of catalytic domains, comparing against the CAZy database, and focusing on families with β-galactosidases activity (GH1, GH2 and GH42). A total of 394 candidate genes were found, all belonging to bacterial species. From these candidates, 12 were selected to be cloned and expressed. A total of six enzymes were expressed, and five cleaved efficiently ortho-nitrophenyl-β-galactoside and lactose. The activity levels of one of these novel β-galactosidase was higher than other enzymes reported from functional metagenomics screening and higher than the only enzyme reported from sequence-based metagenomics. A group of novel mesophilic β-galactosidases from diary stabilization ponds' metagenomes was successfully identified, cloned and expressed. These novel enzymes provide alternatives for the production of value-added products from dairy industries' by-products.
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50
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Extracellular DNA (eDNA): Neglected and Potential Sources of Antibiotic Resistant Genes (ARGs) in the Aquatic Environments. Pathogens 2020; 9:pathogens9110874. [PMID: 33114079 PMCID: PMC7690795 DOI: 10.3390/pathogens9110874] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/11/2020] [Accepted: 10/20/2020] [Indexed: 11/17/2022] Open
Abstract
Over the past decades, the rising antibiotic resistance bacteria (ARB) are continuing to emerge as a global threat due to potential public health risk. Rapidly evolving antibiotic resistance and its persistence in the environment, have underpinned the need for more studies to identify the possible sources and limit the spread. In this context, not commonly studied and a neglected genetic material called extracellular DNA (eDNA) is gaining increased attention as it can be one of the significant drivers for transmission of extracellular ARGS (eARGs) via horizontal gene transfer (HGT) to competent environmental bacteria and diverse sources of antibiotic-resistance genes (ARGs) in the environment. Consequently, this review highlights the studies that address the environmental occurrence of eDNA and encoding eARGs and its impact on the environmental resistome. In this review, we also brief the recent dedicated technological advancements that are accelerating extraction of eDNA and the efficiency of treatment technologies in reducing eDNA that focuses on environmental antibiotic resistance and potential ecological health risk.
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