1
|
Zhou M, Guan X, Deng T, Hu R, Qian L, Yang X, Wu B, Li J, He Q, Shu L, Yan Q, He Z. Synthetic phylogenetically diverse communities promote denitrification and stability. ENVIRONMENTAL RESEARCH 2023; 231:116184. [PMID: 37207729 DOI: 10.1016/j.envres.2023.116184] [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: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.
Collapse
Affiliation(s)
- Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
2
|
Wu B, Guan X, Deng T, Yang X, Li J, Zhou M, Wang C, Wang S, Yan Q, Shu L, He Q, He Z. Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution. Microbiol Spectr 2023; 11:e0452822. [PMID: 37154752 PMCID: PMC10269844 DOI: 10.1128/spectrum.04528-22] [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: 11/07/2022] [Accepted: 04/04/2023] [Indexed: 05/10/2023] Open
Abstract
Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.
Collapse
Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| |
Collapse
|
3
|
Yang X, Yu X, He Q, Deng T, Guan X, Lian Y, Xu K, Shu L, Wang C, Yan Q, Yang Y, Wu B, He Z. Niche differentiation among comammox ( Nitrospira inopinata) and other metabolically distinct nitrifiers. Front Microbiol 2022; 13:956860. [PMID: 36187961 PMCID: PMC9515657 DOI: 10.3389/fmicb.2022.956860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.
Collapse
Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, United States
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| |
Collapse
|
4
|
Hua Z, Jiang C, Song S, Tian D, Chen Z, Jin Y, Zhao Y, Zhou J, Zhang Z, Huang L, Yuan Y. Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence. Mol Ecol Resour 2022; 23:106-117. [PMID: 35951477 DOI: 10.1111/1755-0998.13697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022]
Abstract
Accurate identification of plants remains a significant challenge for taxonomists and is the basis for plant diversity conservation. Although DNA barcoding methods are commonly used for plant identification, these are limited by the low amplification success and low discriminative power of selected genomic regions. In this study, we developed a k-mer-based approach, the DNA signature sequence (DSS), to accurately identify plant taxon-specific markers, especially at the species level. DSS is a constant-length nucleotide sequence capable of identifying a taxon and distinguishing it from other taxa. In this study, we performed the first large-scale study of DSS markers in plants. DSS candidates of 3,899 angiosperm plant species were calculated based on a chloroplast dataset with 4,356 assemblies. Using Sanger sequencing of PCR amplicons and high-throughput sequencing, DSSs were validated in four and 165 species, respectively. Based on this, the universality of the DSSs was over 79.38%. Several indicators influencing DSS marker identification and detection have also been evaluated, and common criteria for DSS application in plant identification have been proposed.
Collapse
Affiliation(s)
- Zhongyi Hua
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Shuhui Song
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Dongmei Tian
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Ziyuan Chen
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yan Jin
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yuyang Zhao
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Junhui Zhou
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Zhang Zhang
- China National Center for Bioinformation, 100101, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| | - Yuan Yuan
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences (CACMS), Beijing 100700, China
| |
Collapse
|
5
|
Wang Q, Ren Y, Cui Y, Gao B, Zhang H, Jiang Q, Loor JJ, Deng Z, Xu C. Bacillus subtilis Produces Amino Acids to Stimulate Protein Synthesis in Ruminal Tissue Explants via the Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Beta–Serine/Threonine Kinase–Mammalian Target of Rapamycin Complex 1 Pathway. Front Vet Sci 2022; 9:852321. [PMID: 35832333 PMCID: PMC9272757 DOI: 10.3389/fvets.2022.852321] [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: 01/11/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
Background Bacillus subtilis is a probiotic strain that is widely used as a feed supplement for ruminants. In this study, one B. subtilis strain isolated from the ruminal fluid of Holstein dairy cows was used for an ex vivo study with ruminal tissue explants. The main goal was to assess the potential endosymbiotic links between B. subtilis and the ruminal epithelium using molecular analyses and amino acid profiling. The explant culture protocol was first optimized to determine the ideal conditions in terms of tissue viability before performing the actual experiments involving active and inactive bacteria with or without protein synthesis inhibitors, such as LY294002 (phosphatidylinositol 3-kinase inhibitor) or rapamycin [mammalian target of rapamycin (mTOR) inhibitor]. Results The mRNA levels of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta (PIK3CB), serine/threonine kinase (AKT), mTOR, P70S6K1, and eukaryotic translation initiation factor 4E binding protein 1 were the highest (p < 0.01), while those of programmed cell death 4 were the lowest when the tissue was incubated with 107 of B. subtilis. Compared with the inactivated bacteria, the expression levels of PIK3CB and AKT, and overall changes in mTOR and P70S6K1 were greater in rumen explants with living bacteria (p < 0.05). With an increase in B. subtilis concentration, the trends of protein and corresponding gene changes were consistent. There were differences in the concentrations of individual amino acids in the supernatants of living and inactivated bacterial culture groups, with most amino acids enriched in pathways, such as aminoacyl tRNA biosynthesis, cyanoamino acid metabolism, monobactam biosynthesis, or glycine, serine, and threonine metabolism. The addition of psilocybin upregulated the expression levels of PIK3CB and AKT. A significant decrease (p < 0.05) in PIK3CB and mTOR protein expression levels was detected after the addition of LY294002 and rapamycin. In addition, These responses were associated with the downregulation (p < 0.05) of AKT and P70S6K protein expression levels. Conclusions We confirmed that the in vivo ruminal tissue culture system is a suitable model for studying probiotic-induced alterations in tissue function. As such, this study provides a means for future mechanistic studies related to microbial regulation and the dietary supply of proteins. In addition, living and inactivated B. subtilis can promote protein synthesis in ruminal tissue explants by altering the expression levels of related factors in the PIK3CB–AKT–mTORC1 pathway, which could further aid in optimizing the feed efficiency and increasing the use of inactivated bacteria as additives in dairy cow farming.
Collapse
Affiliation(s)
- Qiuju Wang
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yulong Ren
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yizhe Cui
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Bingnan Gao
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hao Zhang
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qianming Jiang
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Juan J. Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Zhaoju Deng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chuang Xu
- College of Animal Science and Veterinary, Heilongjiang Bayi Agricultural University, Daqing, China
- *Correspondence: Chuang Xu ;
| |
Collapse
|
6
|
Macroecological distributions of gene variants highlight the functional organization of soil microbial systems. THE ISME JOURNAL 2022; 16:726-737. [PMID: 34580430 PMCID: PMC8857198 DOI: 10.1038/s41396-021-01120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.
Collapse
|
7
|
Species-specific genomic sequences for classification of bacteria. Comput Biol Med 2020; 123:103874. [PMID: 32658789 DOI: 10.1016/j.compbiomed.2020.103874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/04/2020] [Accepted: 06/20/2020] [Indexed: 02/04/2023]
Abstract
Modern bacterial classification relies on genomic relatedness. Genetic variation in bacterial populations present a big challenge for taxonomic classification and recently several bacterial species have been reclassified based on the intra-species genome comparison. These were facilitated by next generation sequencing technologies and advances in genome comparison approaches which led to the rearrangement of diverse bacterial species and revolution in the microbial classification system. One of the outcome of these studies is the development of suitable DNA barcodes as reliable and cost-effective method for identifying various bacterial genera. Towards refining this further, we have applied a genome comparison approach in 1104 bacterial genome assemblies (excluding plasmids) to identify unique genomic segments among intra-species genome assemblies. Using extensive bioinformatics analysis, we have identified species-specific genomic regions and designed unique primers for 100 different species (belonging to 62 genera) which includes 62 pathogenic and 13 opportunistic pathogenic bacterial species and built a database (http://slsdb.manipal.edu/bact/). These species-specific genomic regions will have a major impact on in silico and molecular methods aimed at bacterial classification and identification. These may also serve as better DNA barcodes than the markers currently used for delineation of bacteria and may also find application in various translational research programs.
Collapse
|
8
|
Panyukov VV, Kiselev SS, Ozoline ON. Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling. Int J Mol Sci 2020; 21:ijms21030944. [PMID: 32023871 PMCID: PMC7037511 DOI: 10.3390/ijms21030944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/21/2020] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn's disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific "barcodes" for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.
Collapse
Affiliation(s)
- Valery V. Panyukov
- Institute of Mathematical Problems of Biology RAS—the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, 142290 Pushchino, Russia;
- Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
| | - Sergey S. Kiselev
- Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
- Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Olga N. Ozoline
- Structural and Functional Genomics Group, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
- Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| |
Collapse
|
9
|
Escalas A, Troussellier M, Yuan T, Bouvier T, Bouvier C, Mouchet MA, Flores Hernandez D, Ramos Miranda J, Zhou J, Mouillot D. Functional diversity and redundancy across fish gut, sediment and water bacterial communities. Environ Microbiol 2017; 19:3268-3282. [PMID: 28618142 DOI: 10.1111/1462-2920.13822] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/07/2017] [Indexed: 11/26/2022]
Abstract
This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.
Collapse
Affiliation(s)
- Arthur Escalas
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Marc Troussellier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Thierry Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Corinne Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Maud A Mouchet
- UMR 7204 CESCO, Muséum d'Histoire Naturelle, 55 rue Buffon, Paris, 75005, France
| | - Domingo Flores Hernandez
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Julia Ramos Miranda
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - David Mouillot
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| |
Collapse
|
10
|
Tu Q, Li J, Shi Z, Chen Y, Lin L, Li J, Wang H, Yan J, Zhou Q, Li X, Li L, Zhou J, He Z. HuMiChip2 for strain level identification and functional profiling of human microbiomes. Appl Microbiol Biotechnol 2016; 101:423-435. [PMID: 27734124 DOI: 10.1007/s00253-016-7910-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/18/2016] [Accepted: 09/27/2016] [Indexed: 01/20/2023]
Abstract
With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes. Computational evaluation of strain-specific probes suggested that they were not only specific to mock communities of sequenced microorganisms and metagenomes from different human body sites but also to non-sequenced microbial strains. Experimental evaluation of strain-specific probes using single strains/species and mock communities suggested a high specificity of these probes with their corresponding targets. Application of HuMiChip2 to human gut microbiome samples showed the patient microbiomes of alcoholic liver cirrhosis significantly (p < 0.05) shifted their functional structure from the healthy individuals, and the relative abundance of 21 gene families significantly (p < 0.1) differed between the liver cirrhosis patients and healthy individuals. At the strain level, five Bacteroides strains were significantly (p < 0.1) and more frequently detected in liver cirrhosis patients. These results suggest that the developed HuMiChip2 is a useful microbial ecological microarray for both strain-level identification and functional profiling of human microbiomes.
Collapse
Affiliation(s)
- Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, China.,Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China.,Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Jiabao Li
- Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China
| | - Zhou Shi
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yanfei Chen
- The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lu Lin
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, China
| | - Juan Li
- College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Hongling Wang
- Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China
| | - Jianbo Yan
- Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, Zhejiang, China
| | - Qingming Zhou
- College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Xiangzhen Li
- Chinese Academy of Sciences, Chengdu Institute of Biology, Chengdu, Sichuan, China
| | - Lanjuan Li
- The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
| |
Collapse
|
11
|
Parisot N, Peyretaillade E, Dugat-Bony E, Denonfoux J, Mahul A, Peyret P. Probe Design Strategies for Oligonucleotide Microarrays. Methods Mol Biol 2016; 1368:67-82. [PMID: 26614069 DOI: 10.1007/978-1-4939-3136-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in the field of microbial ecology, exploratory probe design strategies must be also implemented to target not-yet-described sequences. To design such probes, two algorithms, KASpOD and HiSpOD, have been developed and they are available via two user-friendly web services. Here, we describe the use of this software necessary for the design of highly effective probes especially in the context of microbial oligonucleotide microarrays by taking into account all the crucial parameters.
Collapse
Affiliation(s)
- Nicolas Parisot
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France
| | - Eric Peyretaillade
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France
| | - Eric Dugat-Bony
- Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, INRA, AgroParisTech, UMR 782, Thiverval-Grignon, France
| | - Jérémie Denonfoux
- Genomic Platform and R&D, Genoscreen, Campus de l'Institut Pasteur, Lille, France
| | | | - Pierre Peyret
- Université d'Auvergne, EA 4678, CIDAM, Clermont Université, BP 10448, F-63000, Clermont-Ferrand, France.
| |
Collapse
|
12
|
Abstract
Since health benefits conferred by probiotics are strain-specific, identification to the strain level is mandatory to allow the monitoring of the presence and the abundance of specific probiotic in a product or in a gastrointestinal tract. Compared to standard plate counts, the reduced duration of the assays and higher specificity makes PCR-based methods (standard PCR and quantitative PCR) very appropriate for detection or quantification of probiotics. Development of strain-specific assay consists of 4 main stages: (1) strain-specific marker identification; (2) construction of potential strain-specific primers; (3) validation on DNA from pure cultures of target and related strains; and (4) validation on spiked samples. The most important and also the most challenging step is the identification of strain-specific sequences, which can be subsequently targeted by specific primers or probes. Such regions can be identified on sequences derived from 16S-23S internally transcribed spacers, randomly amplified polymorphic DNA, representational difference analysis and suppression subtractive hybridisation. Already known phenotypic or genotypic characteristics of the target strain can also be used to develop the strain-specific assay. However, the initial stage of strain-specific assay development can be replaced by comparative genomics analysis of target genome with related genomes in public databases. Advances in whole genome sequencing (WGS) have resulted in a cost reduction for bacterial genome sequencing and consequently have made this approach available to most laboratories. In the present paper I reviewed the available literature on PCR and qPCR assays developed for detection of a specific probiotic strain and discussed future WGS and comparative genomics-based approaches.
Collapse
Affiliation(s)
- P Treven
- 1 University of Ljubljana, Biotechnical Faculty, Institute of Dairy Science and Probiotics, Groblje 3, 1230 Domžale, Slovenia
| |
Collapse
|
13
|
Behzadi P, Ranjbar R, Alavian SM. Nucleic Acid-based approaches for detection of viral hepatitis. Jundishapur J Microbiol 2014; 8:e17449. [PMID: 25789132 PMCID: PMC4350052 DOI: 10.5812/jjm.17449] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/14/2014] [Accepted: 06/14/2014] [Indexed: 12/12/2022] Open
Abstract
CONTEXT To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. RESULTS Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent. CONCLUSIONS Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages.
Collapse
Affiliation(s)
- Payam Behzadi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Corresponding author: Reza Ranjbar, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, IR Iran. Tel: +98-21-88039883, E-mail:
| | - Seyed Moayed Alavian
- Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
| |
Collapse
|
14
|
Tu Q, He Z, Li Y, Chen Y, Deng Y, Lin L, Hemme CL, Yuan T, Van Nostrand JD, Wu L, Zhou X, Shi W, Li L, Xu J, Zhou J. Development of HuMiChip for functional profiling of human microbiomes. PLoS One 2014; 9:e90546. [PMID: 24595026 PMCID: PMC3942451 DOI: 10.1371/journal.pone.0090546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/01/2014] [Indexed: 02/05/2023] Open
Abstract
Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.
Collapse
Affiliation(s)
- Qichao Tu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Yan Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yanfei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ye Deng
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Lu Lin
- Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China
| | - Christopher L. Hemme
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Tong Yuan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Joy D. Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenyuan Shi
- UCLA School of Dentistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jian Xu
- Chinese Academy of Sciences, Qingdao Institute of Bioenergy and Bioprocess Technology, Qingdao, Shandong, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| |
Collapse
|