301
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Shen W, Ren H. TaxonKit: A practical and efficient NCBI taxonomy toolkit. J Genet Genomics 2021; 48:844-850. [PMID: 34001434 DOI: 10.1016/j.jgg.2021.03.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/27/2021] [Indexed: 01/09/2023]
Abstract
The National Center for Biotechnology Information (NCBI) Taxonomy is widely applied in biomedical and ecological studies. Typical demands include querying taxonomy identifier (TaxIds) by taxonomy names, querying complete taxonomic lineages by TaxIds, listing descendants of given TaxIds, and others. However, existed tools are either limited in functionalities or inefficient in terms of runtime. In this work, we present TaxonKit, a command-line toolkit for comprehensive and efficient manipulation of NCBI Taxonomy data. TaxonKit comprises seven core subcommands providing functions, including TaxIds querying, listing, filtering, lineage retrieving and reformatting, lowest common ancestor computation, and TaxIds change tracking. The practical functions, competitive processing performance, scalability with different scales of datasets and good accessibility can facilitate taxonomy data manipulations. TaxonKit provides free access under the permissive MIT license on GitHub, Brewsci, and Bioconda. The documents are also available at https://bioinf.shenwei.me/taxonkit/.
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Affiliation(s)
- Wei Shen
- Institute for Viral Hepatitis, Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
| | - Hong Ren
- Institute for Viral Hepatitis, Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases, Ministry of Education, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
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302
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Lv Z, Dai R, Xu H, Liu Y, Bai B, Meng Y, Li H, Cao X, Bai Y, Song X, Zhang J. The rice histone methylation regulates hub species of the root microbiota. J Genet Genomics 2021; 48:836-843. [PMID: 34391677 DOI: 10.1016/j.jgg.2021.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/20/2021] [Accepted: 06/20/2021] [Indexed: 12/12/2022]
Abstract
Plants have a close relationship with their root microbiota, which comprises a complex microbial network. Histone methylation is an important epigenetic modification influencing multiple plant traits; however, little is known about the role of plant histone methylation in the assembly and network structure of the root microbiota. In this study, we established that the rice (Oryza sativa) histone methylation regulates the structure and composition of the root microbiota, especially the hub species in the microbial network. DJ-jmj703 (defective in histone H3K4 demethylation) and ZH11-sdg714 (defective in H3K9 methylation) showed significant different root microbiota compared with the corresponding wild types at the phylum and family levels, with a consistent increase in the abundance of Betaproteobacteria and a decrease in the Firmicutes. In the root microbial network, 35 of 44 hub species in the top 10 modules in the tested field were regulated by at least one histone methylation-related gene. These observations establish that the rice histone methylation plays a pivotal role in regulating the assembly of the root microbiota, providing insights into the links between plant epigenetic regulation and root microbiota.
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Affiliation(s)
- Zhiyao Lv
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Rui Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoran Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Meng
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China
| | - Haiyan Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xianwei Song
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; INASEED, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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303
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Seasonal Changes in the Distinct Taxonomy and Function of the Gut Microbiota in the Wild Ground Squirrel ( Spermophilus dauricus). Animals (Basel) 2021; 11:ani11092685. [PMID: 34573650 PMCID: PMC8469230 DOI: 10.3390/ani11092685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
Seasonal breeding is a normal phenomenon in which animals adapt to natural selection and reproduce only in specific seasons. Large studies have reported that the gut microbiota is closely related to reproduction. The purpose of this study was to explore the distinct taxonomy and function of the gut microbiota in the breeding and non-breeding seasons of the wild ground squirrel (Spermophilus dauricus). The 16S rRNA gene sequencing technology was utilized to sequence the gut microbiota of the wild ground squirrel. PICRUSt analysis was also applied to predict the function of the gut microbiota. The results suggested that the main components of the gut microbiota in all samples were Firmicutes (61.8%), Bacteroidetes (32.4%), and Proteobacteria (3.7%). Microbial community composition analyses revealed significant differences between the breeding and non-breeding seasons. At the genus level, Alistipes, Mycoplasma, Anaerotruncus, and Odoribacter were more abundant in the non-breeding season, while Blautia and Streptococcus were more abundant in the breeding season. The results of a functional prediction suggested that the relative abundance of functional categories that were related to lipid metabolism, carbohydrate metabolism, and nucleotide metabolism increased in the breeding season. The relative abundance of energy metabolism, transcription, and signal transduction increased in the non-breeding season. Overall, this study found differences in the taxonomy and function of the gut microbiota of the wild ground squirrel between the breeding and non-breeding seasons, and laid the foundation for further studies on the relationship between the gut microbiota and seasonal breeding.
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304
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Han SS, Jeong YS, Choi SK. Current Scenario and Challenges in the Direct Identification of Microorganisms Using MALDI TOF MS. Microorganisms 2021; 9:microorganisms9091917. [PMID: 34576812 PMCID: PMC8466008 DOI: 10.3390/microorganisms9091917] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 01/12/2023] Open
Abstract
MALDI TOF MS-based microbial identification significantly lowers the operational costs because of minimal requirements of substrates and reagents for extraction. Therefore, it has been widely used in varied applications such as clinical, food, military, and ecological research. However, the MALDI TOF MS method is laced with many challenges including its limitation of the reference spectrum. This review briefly introduces the background of MALDI TOF MS technology, including sample preparation and workflow. We have primarily discussed the application of MALDI TOF MS in the identification of microorganisms. Furthermore, we have discussed the current trends for bioaerosol detection using MALDI TOF MS and the limitations and challenges involved, and finally the approaches to overcome these challenges.
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Affiliation(s)
- Sang-Soo Han
- Advanced Defense Science & Technology Research Institute, Agency for Defense Development, Daejeon 34186, Korea;
| | - Young-Su Jeong
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea;
- Correspondence: ; Tel.: +82-42-821-4843; Fax: +82-42-823-3400
| | - Sun-Kyung Choi
- Chem-Bio Technology Center, Agency for Defense Development, Daejeon 34186, Korea;
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305
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Vänni P, Tejesvi MV, Ainonen S, Renko M, Korpela K, Salo J, Paalanne N, Tapiainen T. Delivery mode and perinatal antibiotics influence the predicted metabolic pathways of the gut microbiome. Sci Rep 2021; 11:17483. [PMID: 34471207 PMCID: PMC8410856 DOI: 10.1038/s41598-021-97007-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Delivery mode and perinatal antibiotics influence gut microbiome composition in children. Most microbiome studies have used the sequencing of the bacterial 16S marker gene but have not reported the metabolic function of the gut microbiome, which may mediate biological effects on the host. Here, we used the PICRUSt2 bioinformatics tool to predict the functional profiles of the gut microbiome based on 16S sequencing in two child cohorts. Both Caesarean section and perinatal antibiotics markedly influenced the functional profiles of the gut microbiome at the age of 1 year. In machine learning analysis, bacterial fatty acid, phospholipid, and biotin biosynthesis were the most important pathways that differed according to delivery mode. Proteinogenic amino acid biosynthesis, carbohydrate degradation, pyrimidine deoxyribonucleotide and biotin biosynthesis were the most important pathways differing according to antibiotic exposure. Our study shows that both Caesarean section and perinatal antibiotics markedly influence the predicted metabolic profiles of the gut microbiome at the age of 1 year.
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Affiliation(s)
- Petri Vänni
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland.
| | - Mysore V Tejesvi
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Sofia Ainonen
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
| | - Marjo Renko
- Department of Paediatrics, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Katja Korpela
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
| | - Jarmo Salo
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Niko Paalanne
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Terhi Tapiainen
- PEDEGO (Pediatrics, Dermatology, Gynecology, Obstetrics) Research Unit and Medical Research Center Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
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306
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Jing G, Zhang Y, Liu L, Wang Z, Sun Z, Knight R, Su X, Xu J. A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity. mSystems 2021; 6:e0039421. [PMID: 34254819 PMCID: PMC8407412 DOI: 10.1128/msystems.00394-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Microbiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here, we propose as a solution a search-based microbiome transition network. By traversing a composition-similarity-based network of 177,022 microbiomes, we show that although the compositions are distinct by habitat, each microbiome is on-average only seven neighbors from any other microbiome on Earth, indicating the inherent homology of microbiomes at the global scale. This network is scale-free, suggesting a high degree of stability and robustness in microbiome transition. By tracking the minimum spanning tree in this network, a global roadmap of microbiome dispersal was derived that tracks the potential paths of formulating and propagating microbiome diversity. Such search-based global microbiome networks, reconstructed within hours on just one computing node, provide a readily expanded reference for tracing the origin and evolution of existing or new microbiomes. IMPORTANCE It remains unclear whether and how compositional changes at the "community to community" level among microbiomes are linked to the origin and evolution of global microbiome diversity. Here we propose a microbiome transition model and a network-based analysis framework to describe and simulate the variation and dispersal of the global microbial beta-diversity across multiple habitats. The traversal of a transition network with 177,022 samples shows the inherent homology of microbiome at the global scale. Then a global roadmap of microbiome dispersal derived from the network tracks the potential paths of formulating and propagating microbiome diversity. Such search-based microbiome network provides a readily expanded reference for tracing the origin and evolution of existing or new microbiomes at the global scale.
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Affiliation(s)
- Gongchao Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufeng Zhang
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Lu Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Sun
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rob Knight
- University of California, San Diego, California, USA
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao, Shandong, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
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307
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The role of microbiota-gut-brain axis in neuropsychiatric and neurological disorders. Pharmacol Res 2021; 172:105840. [PMID: 34450312 DOI: 10.1016/j.phrs.2021.105840] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
Emerging evidence indicates that the gut microbiota play a crucial role in the bidirectional communication between the gut and the brain suggesting that the gut microbes may shape neural development, modulate neurotransmission and affect behavior, and thereby contribute to the pathogenesis and/or progression of many neurodevelopmental, neuropsychiatric, and neurological conditions. This review summarizes recent data on the role of microbiota-gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including depression, anxiety, schizophrenia, autism spectrum disorders, Parkinson's disease, migraine, and epilepsy. Also, the involvement of microbiota in gut disorders co-existing with neuropsychiatric conditions is highlighted. We discuss data from both in vivo preclinical experiments and clinical reports including: (1) studies in germ-free animals, (2) studies exploring the gut microbiota composition in animal models of diseases or in humans, (3) studies evaluating the effects of probiotic, prebiotic or antibiotic treatment as well as (4) the effects of fecal microbiota transplantation.
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308
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Chen H, Ma Y, Liu Z, Li J, Li X, Yang F, Qiu M. Circulating microbiome DNA: An emerging paradigm for cancer liquid biopsy. Cancer Lett 2021; 521:82-87. [PMID: 34461180 DOI: 10.1016/j.canlet.2021.08.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
Dysbiosis of the human microbiome has long been reported to be closely associated with various cancers. Accumulating studies have shown that microbial dysbiosis can accelerate tumorigenesis through tumor-promoting inflammation, DNA damage, and inducing immune evasion. Differential composition of microbiome could be novel biomarkers for cancer detection or biomarkers of successful immunotherapy. More importantly, emerging evidence demonstrates that alterations of circulating microbiome DNA (cmDNA) could serve as promising noninvasive biomarkers for cancer detection. It has been reported that distinct circulating bacterial DNA could distinguish prostate cancer, lung cancer, and melanoma patients from healthy populations. Therefore, in this review, we summarized current literature on microbial biomarkers for cancer detection and unraveled the potential of cmDNA as a promising cancer detection tool.
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Affiliation(s)
- Haiming Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Yi Ma
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Zheng Liu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jiawei Li
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Xiao Li
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
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309
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Zhu Y, Li Y, Yang H, He K, Tang K. Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis ( Nipponia nippon). Front Microbiol 2021; 12:723682. [PMID: 34434183 PMCID: PMC8382091 DOI: 10.3389/fmicb.2021.723682] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.
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Affiliation(s)
- Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yudong Li
- Sichuan Province Laboratory for Natural Resources Protection and Sustainable Utilization, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, China
| | - Haiqiong Yang
- Emei Breeding Center for Crested Ibis, Emei, Chengdu, China
| | - Ke He
- College of Animal Sciences and Technology, Zhejiang A&F University, Hangzhou, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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310
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Zhang X, Xu T, Wang X, Geng Y, Zhao N, Hu L, Liu H, Kang S, Xu S. Effect of Dietary Protein Levels on Dynamic Changes and Interactions of Ruminal Microbiota and Metabolites in Yaks on the Qinghai-Tibetan Plateau. Front Microbiol 2021; 12:684340. [PMID: 34434174 PMCID: PMC8381366 DOI: 10.3389/fmicb.2021.684340] [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] [Received: 03/25/2021] [Accepted: 06/30/2021] [Indexed: 12/26/2022] Open
Abstract
To improve performance and optimize rumen function in yaks (Bos grunniens), further knowledge on the appropriate dietary protein levels for ruminal microbiota and the metabolite profiles of yaks in feedlot feeding is necessary. Current understanding of dietary protein requirements, ruminal microbiota, and metabolites is limited. In this study, yaks were fed a low-protein diet (L; 9.64%), middle low-protein diet (ML; 11.25%), middle high-protein diet (MH; 12.48%), or a high-protein diet (H; 13.87%), and the effects of those diets on changes and interactions in ruminal microbiota and metabolites were investigated. Twenty-four female yaks were selected, and the effects on ruminal microbiota and metabolites were investigated using 16s rRNA gene sequencing and gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). Diets containing different protein levels changed the composition of the rumen bacterial community, the H group significantly reduced the diversity of ruminal microbiota (p < 0.05), and the number of shared amplicon sequence variants (ASVs) between the H group and the other three groups was lower, suggesting that the ruminal microbiota community fluctuated more with a high-protein diet. In rumen, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant bacteria at the phylum level, and Bacteroidetes was significantly less abundant in the MH group than in the L and ML groups (p < 0.05). Prevotella_1, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group had the highest abundance at the genus level. Prevotellaceae was enriched in the low-protein groups, whereas Bacteroidales_BS11_gut_group was enriched in the high-protein groups. Rumen metabolite concentrations and metabolic patterns were altered by dietary protein levels: organic acid metabolites, antioxidant-related metabolites, and some plant-derived metabolites showed variation between the groups. Enrichment analysis revealed that significant changes were concentrated in six pathways, including the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and butanoate metabolism. Network analysis showed promotion or restraint relationships between different rumen microbiota and metabolites. Overall, the rumen function was higher in the MH group. This study provides a reference for appropriate dietary protein levels and improves understanding of rumen microbes and metabolites.
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Affiliation(s)
- XiaoLing Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - TianWei Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - XunGang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - YuanYue Geng
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - LinYong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - HongJin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - ShengPing Kang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.,University of Chinese Academy of Sciences, Beijing, China
| | - ShiXiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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311
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Qian M, Liu J, Zhao D, Cai P, Pan C, Jia W, Gao Y, Zhang Y, Zhang N, Zhang Y, Zhang Q, Wu D, Shan C, Zhang M, Schnabl B, Yang S, Shen X, Wang L. Aryl Hydrocarbon Receptor Deficiency in Intestinal Epithelial Cells Aggravates Alcohol-Related Liver Disease. Cell Mol Gastroenterol Hepatol 2021; 13:233-256. [PMID: 34454169 PMCID: PMC8599170 DOI: 10.1016/j.jcmgh.2021.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS The ligand-activated transcription factor, aryl hydrocarbon receptor (AHR) can sense xenobiotics, dietary, microbial, and metabolic cues. Roles of Ahr in intestinal epithelial cells (IECs) have been much less elucidated compared with those in intestinal innate immune cells. Here, we explored whether the IEC intrinsic Ahr could modulate the development of alcohol-related liver disease (ALD) via the gut-liver axis. METHODS Mice with IEC specific Ahr deficiency (AhrΔIEC) were generated and fed with a control or ethanol diet. Alterations of intestinal microbiota and metabolites were investigated by 16S ribosomal RNA sequencing, metagenomics, and untargeted metabolomics. AHR agonists were used to evaluate the therapeutic potentials of intestinal Ahr activation for ALD treatment. RESULTS AhrΔIEC mice showed more severe liver injury after ethanol feeding than control mice. Ahr deficiency in IECs altered the intestinal metabolite composition, creating an environment that promoted the overgrowth of Helicobacter hepaticus and Helicobacter ganmani in the gut, enhancing their translocation to mesenteric lymph nodes and liver. Among the altered metabolites, isobutyric acid was increased in the cecum of ethanol-fed AhrΔIEC mice relative to control mice. Furthermore, both H.hepaticus and isobutyric acid administration aggravated ethanol-induced liver injury in vivo and in vitro. Supplementation with AHR agonists, 6-formylindolo[3,2-b]carbazole and indole-3-carbinol, protected mice from ALD development by specifically activating intestinal Ahr without affecting liver Ahr function. Alcoholic patients showed lower intestinal AHR expression and higher H.hepaticus levels compared with healthy individuals. CONCLUSIONS Our results indicate that targeted restoration of IEC intrinsic Ahr function may present as a novel approach for ALD treatment.
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Affiliation(s)
- Minyi Qian
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China,School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Liu
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China
| | - Danyang Zhao
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China
| | - Pengpeng Cai
- Department of Gastroenterology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Chuyue Pan
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China
| | - Wenxin Jia
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China
| | - Yingsheng Gao
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China
| | - Yufei Zhang
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China
| | - Nan Zhang
- Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yinan Zhang
- Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Quan Zhang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chengjie Shan
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Meiling Zhang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, California
| | - Song Yang
- Department of Hepatology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xu Shen
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lirui Wang
- School of Basic Medicine and Clinical Pharmacy, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,Institute of Modern Biology, Nanjing University, Nanjing, China,Correspondence Address correspondence to: Lirui Wang, PhD, Institute of Modern Biology, Nanjing University, 22 Hankou Road, Gulou District, Nanjing, 210093 China.
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312
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Ling J, Zhou W, Yang Q, Yin J, Zhang J, Peng Q, Huang X, Zhang Y, Dong J. Spatial and Species Variations of Bacterial Community Structure and Putative Function in Seagrass Rhizosphere Sediment. Life (Basel) 2021; 11:life11080852. [PMID: 34440596 PMCID: PMC8401270 DOI: 10.3390/life11080852] [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: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 12/21/2022] Open
Abstract
Seagrasses are an important part of the coral reef ecosystem, and their rhizosphere microbes are of great ecological importance. However, variations in diversity, composition, and potential functions of bacterial communities in the seagrass rhizosphere of coral reef ecosystems remain unclear. This study employed the high-throughput sequencing based on 16S rDNA gene sequences and functional annotation of prokaryotic taxa (FAPROTAX) analysis to investigate these variations based on seagrass species and sampling locations, respectively. Results demonstrated that the seagrass rhizosphere microbial community was mainly dominated by phylum Proteobacteria (33.47%), Bacteroidetes (23.33%), and Planctomycetes (12.47%), while functional groups were mainly composed of sulfate respiration (14.09%), respiration of sulfur compounds (14.24%), aerobic chemoheterotrophy (20.87%), and chemoheterotrophy (26.85%). Significant differences were evident in alpha diversity, taxonomical composition and putative functional groups based on seagrass species and sampling locations. Moreover, the core microbial community of all investigated samples was identified, accounting for 63.22% of all obtained sequences. Network analysis indicated that most microbes had a positive correlation (82.41%), and two module hubs (phylum Proteobacteria) were investigated. Furthermore, a significant positive correlation was found between the OTUs numbers obtained and the functional groups assigned for seagrass rhizosphere microbial communities (p < 0.01). Our result would facilitate future investigation of the function of seagrass rhizosphere microbes.
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Affiliation(s)
- Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya 572000, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 511458, China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya 572000, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 511458, China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya 572000, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 511458, China
| | - Jianping Yin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuying Peng
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhang Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (J.L.); (W.Z.); (Q.Y.); (J.Y.); (J.Z.); (Q.P.); (X.H.); (Y.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, SCSIO, Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya 572000, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 511458, China
- Correspondence: ; Tel.: +86-20-8910-7830
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Zhou A, Xie S, Zhang Y, Chuan J, Tang H, Li X, Zhang L, Xu G, Zou J. Interaction of environmental eukaryotic microorganisms and fungi in the pond-cultured carps: new insights into the potential pathogenic fungi in the freshwater aquaculture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:38839-38854. [PMID: 33745047 DOI: 10.1007/s11356-021-13231-y] [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: 11/26/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The quality and safety of the aquatic products have gradually become the focus of global attention. In this study, the environmental eukaryotic and fungi communities in pond-cultured grass carp (Ctenopharyngodon idellus) and the koi carp (Cyprinus carpio L.) were investigated. For comparative analysis, the alpha diversity shows that the environmental microbial abundance in the koi carp groups were higher than that in the grass carp groups, while beta diversity reveals that the differences of the microbial community composition and structures in the grass carp groups were significantly higher than those in the koi carp groups. Meanwhile, the environmental microbial diversity of grass carp groups was higher than that of koi carp groups at phylum level, but showed no significant difference at genus level. Additionally, the dominant total phyla were Opisthokonta, Stramenopiles plusAlveolates plusRhizaria, Archaeplastida, Cryptophyceae, and Centrohelida for the 18S rRNA gene and Ciliophora, Chlorophyta, and Ascomycota for the ITS2 rRNA gene in both of the two carp groups. Additionally, annotation analysis showed that the biomarkers in the grass carp groups are significantly higher than those of the koi carp groups. Furthermore, the functional prediction of Funguild showed significant difference in outputs, while similarity in trophic modes and guild types between the two carp groups. Meanwhile, the total relative abundances of animal pathogen, fungal parasite, and plant pathogen were extremely similar between the two carp groups. Surprisingly, one pathogenic fungus of genus Fusarium was identified in both the environments of two carp groups based on filtered operational taxonomic unit tables. Overall, this is the first robust report to understand the characteristics of environmental eukaryotic microorganisms and fungi in the edible and ornamental carps. Our results also provide the basic data for the prevention of fungal diseases and the healthy culture of the carps.
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Affiliation(s)
- Aiguo Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shaolin Xie
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Zhang
- Departments of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Jiacheng Chuan
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
| | - Huijuan Tang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xiang Li
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A 5 T1, Canada
| | - Li Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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314
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Wei LQ, Cheong IH, Yang GH, Li XG, Kozlakidis Z, Ding L, Liu NN, Wang H. The Application of High-Throughput Technologies for the Study of Microbiome and Cancer. Front Genet 2021; 12:699793. [PMID: 34394190 PMCID: PMC8355622 DOI: 10.3389/fgene.2021.699793] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
Human gut microbiome research, especially gut microbiome, has been developing at a considerable pace over the last decades, driven by a rapid technological advancement. The emergence of high-throughput technologies, such as genomics, transcriptomics, and others, has afforded the generation of large volumes of data, and in relation to specific pathologies such as different cancer types. The current review identifies high-throughput technologies as they have been implemented in the study of microbiome and cancer. Four main thematic areas have emerged: the characterization of microbial diversity and composition, microbial functional analyses, biomarker prediction, and, lastly, potential therapeutic applications. The majority of studies identified focus on the microbiome diversity characterization, which is reaching technological maturity, while the remaining three thematic areas could be described as emerging.
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Affiliation(s)
- Lu Qi Wei
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Io Hong Cheong
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Huan Yang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Guang Li
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Lei Ding
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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315
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Sheng C, Lin L, Lin H, Wang X, Han Y, Liu SL. Altered Gut Microbiota in Adults with Subjective Cognitive Decline: The SILCODE Study. J Alzheimers Dis 2021; 82:513-526. [PMID: 34024839 DOI: 10.3233/jad-210259] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Subjective cognitive decline (SCD) is the earliest symptomatic manifestation of preclinical Alzheimer's disease (AD). Gut microbiota may serve as a susceptibility factor for AD. Altered gut microbiota has been reported in patients with mild cognitive impairment (MCI) and AD dementia. However, whether gut microbial compositions changed in SCD remains largely unknown. OBJECTIVE To characterize the gut microbiota in SCD. METHODS In this study, a total of 105 participants including 38 normal controls (NC), 53 individuals with SCD, and 14 patients with cognitive impairment (CI) were recruited. Gut microbiota of all participants isolated from fecal samples were investigated using 16S ribosomal RNA (rRNA) Illumina Miseq sequencing technique. The gut microbial compositions were compared among the three groups, and the association between altered gut microbiota and cognitive performance was analyzed. To validate the alteration of gut microbiota in SCD, we conducted amyloid positron emission tomography (PET) in selected participants and further compared the gut microbiota among subgroups. RESULTS The abundance of phylum Firmicutes, class Clostridia, order Clostridiales, family Ruminococcaceae, and genus Faecalibacterium showed a trend toward a progressive decline from NC to SCD and CI. Specifically, the abundance of the anti-inflammatory genus Faecalibacterium was significantly decreased in SCD compared with NC. In addition, altered bacterial taxa among the three groups were associated with cognitive performance. The findings were validated in SCD participants with positive amyloid evidence. CONCLUSION The composition of gut microbiota is altered in individuals with SCD. This preliminary study will provide novel insights into the pathophysiological mechanism of AD.
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Affiliation(s)
- Can Sheng
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Li Lin
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Hua Lin
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xiaoni Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,School of Biomedical Engineering, Hainan University, Haikou, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Shu-Lin Liu
- Genomics Research Center, State-Province Key Laboratories of Biomedicine Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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316
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Zhan S, Li N, Liu C, Mao R, Wu D, Li T, Chen M, Zhuang X, Zeng Z. Intestinal Fibrosis and Gut Microbiota: Clues From Other Organs. Front Microbiol 2021; 12:694967. [PMID: 34335525 PMCID: PMC8322786 DOI: 10.3389/fmicb.2021.694967] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Fibrosis is a complex and difficult to elucidate pathological process with no available therapies. Growing evidence implicates intestinal microbiota in the occurrence and development of fibrosis, and the potential mechanisms involved in different organs have been explored in several studies. In this review, we summarize the causative and preventive effects of gut microbiota on intestinal fibrosis, as well as the relationships between gut microbiota and fibrosis in other organs. Interestingly, several colonized microbes are associated with fibrosis via their structural components and metabolic products. They may also play essential roles in regulating inflammation and fibroblast activation or differentiation, which modulates extracellular matrix formation. While the relationships between intestinal fibrosis and gut microbiota remain unclear, lessons can be drawn from the effects of gut microbiota on hepatic, cardiac, nephritic, and pulmonary fibrosis. Various intestinal microbes alterations have been detected in different fibrotic organs; however, the results were heterogeneous. Mechanisms by which the intestinal microbiota regulate fibrotic processes in other organs, such as novel metabolic products or specific microbes, are also discussed. The specific microbiota associated with fibrosis in other organs could instruct future studies aiming to discover prospective mechanisms regulating intestinal fibrosis.
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Affiliation(s)
- Shukai Zhan
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Na Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Caiguang Liu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ren Mao
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dongxuan Wu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tong Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaojun Zhuang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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317
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Sola-Leyva A, Andrés-León E, Molina NM, Terron-Camero LC, Plaza-Díaz J, Sáez-Lara MJ, Gonzalvo MC, Sánchez R, Ruíz S, Martínez L, Altmäe S. Mapping the entire functionally active endometrial microbiota. Hum Reprod 2021; 36:1021-1031. [PMID: 33598714 DOI: 10.1093/humrep/deaa372] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/11/2020] [Indexed: 12/13/2022] Open
Abstract
STUDY QUESTION Does endometrium harbour functionally active microorganisms and whether the microbial composition differs between proliferative and mid-secretory phases? SUMMARY ANSWER Endometrium harbours functionally alive microorganisms including bacteria, viruses, archaea and fungi whose composition and metabolic functions change along the menstrual cycle. WHAT IS KNOWN ALREADY Resident microbes in the endometrium have been detected, where microbial dysfunction has been associated with reproductive health and disease. Nevertheless, the core microorganismal composition in healthy endometrium is not determined and whether the identified bacterial DNA sequences refer to alive/functionally active microbes is not clear. Furthermore, whether there are cyclical changes in the microbial composition remains an open issue. STUDY DESIGN, SIZE, DURATION RNA sequencing (RNAseq) data from 14 endometrial paired samples from healthy women, 7 samples from the mid-secretory phase and 7 samples from the consecutive proliferative phase were analysed for the microbial RNA sequences. PARTICIPANTS/MATERIALS, SETTING, METHODS The raw RNAseq data were converted into FASTQ format using SRA Toolkit. The unmapped reads to human sequences were aligned to the reference database Kraken2 and visualised with Krona software. Menstrual phase taxonomic differences were performed by R package metagenomeSeq. The functional analysis of endometrial microbiota was obtained with HUMANn2 and the comparison between menstrual phases was conducted by one-way ANOVA. Human RNAseq analysis was performed using miARma-Seq and the functional enrichment analysis was carried out using gene set enrichment analysis (GSEA; HumanCyc). The integration of metabolic pathways between host and microbes was investigated. The developed method of active microbiota mapping was validated in independent sample set. MAIN RESULTS AND THE ROLE OF CHANCE With the novel metatranscriptomic approach, we mapped the entire alive microbiota composing of >5300 microorganisms within the endometrium of healthy women. Microbes such as bacteria, fungi, viruses and archaea were identified. The validation of three independent endometrial samples from different ethnicity confirmed the findings. Significant differences in the microbial abundances in the mid-secretory vs. proliferative phases were detected with possible metabolic activity in the host-microbiota crosstalk in receptive phase endometrium, specifically in the prostanoid biosynthesis pathway and L-tryptophan metabolism. LARGE SCALE DATA The raw RNAseq data used in the current study are available at GEO GSE86491 and at BioProject PRJNA379542. LIMITATIONS, REASONS FOR CAUTION These pioneering results should be confirmed in a bigger sample size. WIDER IMPLICATIONS OF THE FINDINGS Our study confirms the presence of active microbes, bacteria, fungi, viruses and archaea in the healthy human endometrium with implications in receptive phase endometrial functions, meaning that microbial dysfunction could impair the metabolic pathways important for endometrial receptivity. The results of this study contribute to the better understanding of endometrial microbiota composition in healthy women and its possible role in endometrial functions. In addition, our novel methodological pipeline for analysing alive microbes with transcriptional and metabolic activities could serve to inspire new analysis approaches in reproductive medicine. STUDY FUNDING/COMPETING INTERESTS This work is supported by the Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER): grants RYC-2016-21199 and ENDORE SAF2017-87526-R; FEDER/Junta de Andalucía-Consejería de Economía y Conocimiento: MENDO (B-CTS-500-UGR18) and by the University of Granada Plan Propio de Investigación 2016 - Excellence actions: Unit of Excellence on Exercise and Health (UCEES) (SOMM17/6107/UGR). A.S.-L. and N.M.M. are funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-0854409 and FPU19/01638). S.A. has received honoraria for lectures from Merck. The funder had no role in this study.
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Affiliation(s)
- Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Eduardo Andrés-León
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada 18016, Spain
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Laura Carmen Terron-Camero
- Unidad de Bioinformática, Instituto de Parasitología y Biomedicina "López-Neyra", CSIC (IPBLN-CSIC), Granada 18016, Spain
| | - Julio Plaza-Díaz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada 18071, Spain.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - María José Sáez-Lara
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Institute of Nutrition and Food Technology (INYTA), "José Mataix Verdú" Biomedical Research Centre (CIBM), University of Granada, Armilla, Granada 18016, Spain
| | - María Carmen Gonzalvo
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Rocío Sánchez
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Susana Ruíz
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Luís Martínez
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Unidad Reproducción, UGC Laboratorio clínico y UGC Obstetricia y Ginecología. Hospital Universitario Virgen de las Nieves, Granada 18014, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain.,Competence Centre on Health Technologies, Tartu 50411, Estonia
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318
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Survey of artificial intelligence approaches in the study of anthropogenic impacts on symbiotic organisms – a holistic view. Symbiosis 2021. [DOI: 10.1007/s13199-021-00778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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319
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Variations in Gut Microbiome are Associated with Prognosis of Hypertriglyceridemia-Associated Acute Pancreatitis. Biomolecules 2021; 11:biom11050695. [PMID: 34066441 PMCID: PMC8148198 DOI: 10.3390/biom11050695] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Hypertriglyceridemia-associated acute pancreatitis (HTGAP) is linked with increased severity and morbidity. Intestinal flora plays an important role in the progression of acute pancreatitis (AP). However, pathogenetic association between gut microbiota and HTGAP remains unknown. In this study, we enrolled 30 HTGAP patients and 30 patients with AP that is evoked by other causes. The V3–V4 regions of 16S rRNA sequences of the gut microbiota were analyzed. Clinical characteristics, microbial diversity, taxonomic profile, microbiome composition, microbiological phenotype, and functional pathways were compared between the two groups. Our results showed that the HTGAP group had a higher proportion of severe AP (46.7% vs. 20.0%), organ failure (56.7% vs. 30.0%), and a longer hospital stay (18.0 days vs. 6.5 days). HTGAP group also had poorer microbial diversity, higher abundances of Escherichia/Shigella and Enterococcus, but lower abundances of Dorea longicatena, Blautia wexlerae, and Bacteroides ovatus as compared with non-HTGAP group. Correlation analysis revealed that gut bacterial taxonomic and functional changes were linked with local and systemic complications, ICU admission, and mortality. This study revealed that alterations of gut microbiota were associated with disease severity and poor prognosis in HTGAP patients, indicating a potential pathophysiological link between gut microbiota and hypertriglyceridemia related acute pancreatitis.
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320
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Cheung H, Yu J. Machine learning on microbiome research in gastrointestinal cancer. J Gastroenterol Hepatol 2021; 36:817-822. [PMID: 33880761 DOI: 10.1111/jgh.15502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Gastrointestinal cancer maintains the highest incidence and mortality rate among all cancers globally. In addition to genetic causes, it has been reported that individuals' diet and composition of the gastrointestinal microbiome have profound impacts on gastrointestinal cancer development. Microbiome research has risen in popularity to provide alternative insights into cancer development and potential therapeutic effect. However, there is a lack of an effective analytical tool to comprehend the massive amount of data generated from high-throughput sequencing methods. Artificial intelligence is another rapidly developing field that has strong application potential in microbiome research. Deep learning and machine learning are two subfields under the umbrella of artificial intelligence. Here we discuss the current approaches to study the gut microbiome, as well as the applications and challenges of implementing artificial intelligence in microbiome research.
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Affiliation(s)
- Henley Cheung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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321
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Hu X, Li H, Zhao X, Zhou R, Liu H, Sun Y, Fan Y, Shi Y, Qiao S, Liu S, Liu H, Zhang S. Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome. Theranostics 2021; 11:5778-5793. [PMID: 33897881 PMCID: PMC8058718 DOI: 10.7150/thno.55946] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Rationale: Prior chronic treatment with statins has been shown to be associated with more favorable outcomes in patients with acute coronary syndrome (ACS). Specific changes in the gut microbiota and microbial metabolites have been shown to influence the progression of coronary artery disease. However, the critical microbial and metabolomic changes associated with the cardiovascular protective effects of statins in ACS remain elusive. Methods: In the present study, we performed 16S rRNA sequencing and serum metabolomic analysis in 36 ACS patients who had received chronic statin treatment, 67 ACS patients who had not, and 30 healthy volunteers. A follow-up study was conducted. Metagenomic functional prediction of important bacterial taxa was achieved using PICRUSt2. Results: Statins modulated the gut microbiome of ACS patients towards a healthier status, i.e., reducing potentially pathogenic bacteria such as Parabacteroides merdae but increasing beneficial bacteria such as Bifidobacterium longum subsp. longum, Anaerostipes hadrus and Ruminococcus obeum. Moreover, prior chronic statin therapy was associated with improved outcome in ACS patients. Multi-omics analysis revealed that specific changes in bacterial taxa were associated with disease severity or outcomes either directly or by mediating metabolites such as fatty acids and prenol lipids. Finally, we discovered that important taxa associated with statins were correlated with fatty acid- and isoprenoid-related pathways that were predicted by PICRUSt2. Conclusions: Our study suggests that statin treatment might benefit ACS patients by modulating the composition and function of the gut microbiome, which might result in improved circulating metabolites and reduced metabolic risk. Our findings provide new insights for understanding the heterogenic roles of statins in ACS patients through host gut microbiota metabolic interactions.
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Affiliation(s)
- Xiaomin Hu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Hanyu Li
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Xinyue Zhao
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Ruilin Zhou
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Honghong Liu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Yueshen Sun
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Yue Fan
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Yanan Shi
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
| | - Shanshan Qiao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
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322
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Bo TB, Kohl KD. Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry. Anim Microbiome 2021; 3:26. [PMID: 33785073 PMCID: PMC8011129 DOI: 10.1186/s42523-021-00087-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness. In addition to the bacteria transmitted from the mother to offspring, microbes from the surrounding environment also account for a large proportion of the developing gut microbiome. While it was long believed that microbial species all have global distributions, we now know that there are substantial geographic differences and dispersal limitations to environmental microbes. The establishment of gut microbiota during early life has enormous impacts on animal development, including energy metabolism, training of the immune system, and cognitive development. Moreover, these microbial effects scale to influence animal performance and fitness, raising the possibility for natural selection to act on the integrated combination of gut microbial communities and host genetics (i.e. the holobiont). Therefore, in this paper, we propose a hypothesis: that optimization of host-microbe-environment interactions represents a potentially important yet overlooked reason for natal philopatry. Microbiota obtained by natal philopatry could help animals adapt to the environment and improve the survival rates of their young. We propose future directions to test these ideas, and the implications that this hypothesis has for our understanding of host-microbe interactions.
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Affiliation(s)
- Ting-Bei Bo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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323
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Pang Z, Chen J, Wang T, Gao C, Li Z, Guo L, Xu J, Cheng Y. Linking Plant Secondary Metabolites and Plant Microbiomes: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:621276. [PMID: 33737943 PMCID: PMC7961088 DOI: 10.3389/fpls.2021.621276] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/08/2021] [Indexed: 05/09/2023]
Abstract
Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia Chen
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhimin Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Litao Guo
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianping Xu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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324
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Zhao C, Su W, Mu Y, Mu Y, Jiang L. Integrative Metagenomics-Metabolomics for Analyzing the Relationship Between Microorganisms and Non-volatile Profiles of Traditional Xiaoqu. Front Microbiol 2021; 11:617030. [PMID: 33597930 PMCID: PMC7882485 DOI: 10.3389/fmicb.2020.617030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
Xiaoqu, one of three traditional jiuqu in China, is a saccharifying and fermenting agent used in Xiaoqu jiu brewing, with different ingredient compositions and preparation techniques used in various regions. The yield and quality of Xiaoqu jiu are significantly affected by the metabolites and microbiota of Xiaoqu; however, the associated relationship remains poorly understood. This study aimed to analyze this relationship in three typical traditional Xiaoqu from the Guizhou province in China. The non-volatile metabolites of Xiaoqu were detected using gas chromatography time-of-flight mass spectrometry, whereas the classification and metabolic potential of the microbiota were investigated using metagenomic sequencing. Results show that Firmicutes, Proteobacteria, and Actinobacteria represent the dominant bacterial phyla, with Lactobacillus, Bacillus, Acinetobacter, Leuconostoc, and Weissella found to be the dominant bacterial genera. Meanwhile, Ascomycota, Mucoromycota, and Basidiomycota are the dominant fungal phyla with Aspergillus, Saccharomyces, Pichia, Rhizopus, and Phycomyces being the predominant fungal genera. Functional annotation of the microbiota revealed a major association with metabolism of carbohydrates, cofactors, and vitamins, as well as amino acids. A total of 39 significantly different metabolites (SDMs) were identified that are involved in 47 metabolic pathways, primarily that of starch and sucrose; glycine, serine, and threonine; glyoxylate and dicarboxylate; pyruvate; as well as biosynthesis of pantothenate and CoA. Further, based on Spearman's correlation analysis, Aspergillus, Saccharomyces, Lactobacillus, Acetobacter, Weissella, Pantoea, Desmospora, and Bacillus are closely correlated with production of physicochemical indexes and SDMs. Moreover, the metabolic network generated for the breakdown of substrates and formation of SDMs in Xiaoqu was found to primarily center on the metabolism of carbohydrates and the tricarboxylic acid cycle. These results provide insights into the functional microorganisms and metabolic patterns present in traditional Guizhou Xiaoqu and might guide researchers in the production of stable and efficient Xiaoqu in the future.
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Affiliation(s)
- Chi Zhao
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Storage and Processing of Agricultural and Animal Products, Guizhou University, Guiyang, China
| | - Wei Su
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Storage and Processing of Agricultural and Animal Products, Guizhou University, Guiyang, China
| | - Yu Mu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China.,Guizhou Key Laboratory for Storage and Processing of Agricultural and Animal Products, Guizhou University, Guiyang, China
| | - Yingchun Mu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Li Jiang
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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325
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Molina NM, Sola-Leyva A, Haahr T, Aghajanova L, Laudanski P, Castilla JA, Altmäe S. Analysing endometrial microbiome: methodological considerations and recommendations for good practice. Hum Reprod 2021; 36:859-879. [DOI: 10.1093/humrep/deab009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
There is growing evidence that the upper female genital tract is not sterile, harbouring its own microbial communities. However, the significance and the potential effect of endometrial microorganisms on reproductive functions remain to be fully elucidated. Analysing the endometrial microbiome, the microbes and their genetic material present in the endometrium, is an emerging area of study. The initial studies suggest it is associated with poor reproductive outcomes and with different gynaecological pathologies. Nevertheless, studying a low-biomass microbial niche as is endometrium, the challenge is to conduct well-designed and well-controlled experiments in order to avoid and adjust for the risk of contamination, especially from the lower genital tract. Herein, we aim to highlight methodological considerations and propose good practice recommendations for future endometrial microbiome studies.
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Affiliation(s)
- Nerea M Molina
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
| | - Thor Haahr
- The Fertility Clinic, Skive Regional Hospital, Skive 7800, Denmark
| | - Lusine Aghajanova
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Stanford School of Medicine, Sunnyvale, CA 94087, USA
| | - Piotr Laudanski
- Department of Obstetrics and Gynecology, Medical University of Warsaw, Warsaw 02-015, Poland
| | - Jose Antonio Castilla
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Unidad de Reproducción, UGC de Obstetricia y Ginecología, Hospital Universitario Virgen de las Nieves, Granada 18012, Spain
- CEIFER Biobanco—NextClinics, Granada 18004, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada 18071, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada 18014, Spain
- Competence Centre on Health Technologies, Tartu 50410, Estonia
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326
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Gong T, Xin XF. Phyllosphere microbiota: Community dynamics and its interaction with plant hosts. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:297-304. [PMID: 33369158 DOI: 10.1111/jipb.13060] [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: 08/07/2020] [Accepted: 12/17/2020] [Indexed: 05/22/2023]
Abstract
Plants are colonized by various microorganisms in natural environments. While many studies have demonstrated key roles of the rhizosphere microbiota in regulating biological processes such as nutrient acquisition and resistance against abiotic and biotic challenges, less is known about the role of the phyllosphere microbiota and how it is established and maintained. This review provides an update on current understanding of phyllosphere community assembly and the mechanisms by which plants and microbes establish the phyllosphere microbiota for plant health.
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Affiliation(s)
- Tianyu Gong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Fang Xin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The Chinese Academy of Sciences (CAS) and CAS John Innes Centre of Excellence for Plant and Microbial Sciences, Shanghai, 200032, China
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327
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Zhang J, Liu YX, Guo X, Qin Y, Garrido-Oter R, Schulze-Lefert P, Bai Y. High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat Protoc 2021; 16:988-1012. [PMID: 33442053 DOI: 10.1038/s41596-020-00444-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 10/13/2020] [Indexed: 01/29/2023]
Abstract
Cultivating native bacteria from roots of plants grown in a given environment is essential for dissecting the functions of the root microbiota for plant growth and health with strain-specific resolution. In this study, we established a straightforward protocol for high-throughput bacterial isolation from fresh root samples using limiting dilution to ensure that most cultured bacteria originated from only one microorganism. This is followed by strain characterization using a two-sided barcode polymerase chain reaction system to identify pure and heterogeneous bacterial cultures. Our approach overcomes multiple difficulties of traditional bacterial isolation and identification methods, such as obtaining bacteria with diverse growth rates while greatly increasing throughput. To facilitate data processing, we developed an easy-to-use bioinformatic pipeline called 'Culturome' ( https://github.com/YongxinLiu/Culturome ) and a graphical user interface web server ( http://bailab.genetics.ac.cn/culturome/ ). This protocol allows any research group (two or three lab members without expertise in bioinformatics) to systematically cultivate root-associated bacteria within 8-9 weeks.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yong-Xin Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxuan Guo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuan Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ruben Garrido-Oter
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .,CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China. .,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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328
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Massimino L, Lovisa S, Antonio Lamparelli L, Danese S, Ungaro F. Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? Comput Struct Biotechnol J 2020; 19:16-28. [PMID: 33363706 PMCID: PMC7750180 DOI: 10.1016/j.csbj.2020.11.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is composed of bacteria and viruses that might be associated with colorectal cancer (CRC) onset and progression. Indeed, although viral infections have been reported to be the primary trigger in many diseases, the role of eukaryotic viruses populating the gut mucosa during early colorectal carcinogenesis is underinvestigated. Human eukaryotic viruses in the gut were found to induce alterations of the immune homeostasis so that some viral-dependent mechanisms likely able to induce DNA alterations in the bowel wall have been proposed, although no demonstration is available yet. However, thanks to the latest advancements in computational biology and the implementation of the bioinformatic pipelines, the option of establishing a direct causative link between intestinal virome and CRC will be possible soon, hopefully paving the way to innovative therapeutic strategies blocking or reverting the CRC pathogenesis.
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Affiliation(s)
- Luca Massimino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Sara Lovisa
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | | | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Federica Ungaro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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329
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Bokulich NA, Ziemski M, Robeson MS, Kaehler BD. Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. Comput Struct Biotechnol J 2020; 18:4048-4062. [PMID: 33363701 PMCID: PMC7744638 DOI: 10.1016/j.csbj.2020.11.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022] Open
Abstract
Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective study of microbiomes (microbiomics) relies on the development, optimization, and validation of computational methods for analyzing microbial datasets, such as from marker-gene (e.g., 16S rRNA gene) and metagenome data. This review describes best practices for benchmarking and implementing computational methods (and software) for studying microbiomes, with particular focus on unique characteristics of microbiomes and microbiomics data that should be taken into account when designing and testing microbiomics methods.
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Affiliation(s)
- Nicholas A. Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zurich, Switzerland
| | - Michal Ziemski
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition, and Health, ETH Zurich, Switzerland
| | - Michael S. Robeson
- University of Arkansas for Medical Sciences, Department of Biomedical Informatics, Little Rock, AR, USA
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330
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Zhuang W, Yu X, Hu R, Luo Z, Liu X, Zheng X, Xiao F, Peng Y, He Q, Tian Y, Yang T, Wang S, Shu L, Yan Q, Wang C, He Z. Diversity, function and assembly of mangrove root-associated microbial communities at a continuous fine-scale. NPJ Biofilms Microbiomes 2020; 6:52. [PMID: 33184266 PMCID: PMC7665043 DOI: 10.1038/s41522-020-00164-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Mangrove roots harbor a repertoire of microbial taxa that contribute to important ecological functions in mangrove ecosystems. However, the diversity, function, and assembly of mangrove root-associated microbial communities along a continuous fine-scale niche remain elusive. Here, we applied amplicon and metagenome sequencing to investigate the bacterial and fungal communities among four compartments (nonrhizosphere, rhizosphere, episphere, and endosphere) of mangrove roots. We found different distribution patterns for both bacterial and fungal communities in all four root compartments, which could be largely due to niche differentiation along the root compartments and exudation effects of mangrove roots. The functional pattern for bacterial and fungal communities was also divergent within the compartments. The endosphere harbored more genes involved in carbohydrate metabolism, lipid transport, and methane production, and fewer genes were found to be involved in sulfur reduction compared to other compartments. The dynamics of root-associated microbial communities revealed that 56-74% of endosphere bacterial taxa were derived from nonrhizosphere, whereas no fungal OTUs of nonrhizosphere were detected in the endosphere. This indicates that roots may play a more strictly selective role in the assembly of the fungal community compared to the endosphere bacterial community, which is consistent with the projections established in an amplification-selection model. This study reveals the divergence in the diversity and function of root-associated microbial communities along a continuous fine-scale niche, thereby highlighting a strictly selective role of soil-root interfaces in shaping the fungal community structure in the mangrove root systems.
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Affiliation(s)
- Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, S9H 3×2, Canada
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), South China Sea Institution, Sun Yat-sen University, 510006, Guangzhou, China.
- College of Agronomy, Hunan Agricultural University, 410128, Changsha, China.
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331
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Zuo HJ, Fu MR, Zhao HL, Du XW, Hu ZY, Zhao XY, Ji XQ, Feng XQ, Zhumajiang W, Zhou TH, Tian YL, Pei XF, Yu R, Hu XY. Study on the Salivary Microbial Alteration of Men With Head and Neck Cancer and Its Relationship With Symptoms in Southwest China. Front Cell Infect Microbiol 2020; 10:514943. [PMID: 33244461 PMCID: PMC7685052 DOI: 10.3389/fcimb.2020.514943] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 10/15/2020] [Indexed: 02/05/2023] Open
Abstract
This study explored the association between oral microbes and head and neck cancer (HNC) as well as symptoms related to patients with HNC before surgical treatment. Fifty-six patients with HNC and 64 matched healthy controls were recruited from West China hospital in Southwest China. The demographic, clinical, and symptom data were collected. Salivary samples were collected to determine the microbial characteristics using 16S rRNA gene sequencing. Patients with HNC presented increased Capnocytophaga abundances. The oral microbial markers as Capnocytophaga (area under the curve=0.81) achieved a high classification power between the HNC patients and healthy controls. Moreover, using Capnocytophaga in conjunction with symptom of voice/speech difficulty achieved an overall predicting accuracy of 92.5% comparing with using Capnocytophaga alone (79.2% accuracy) in distinguishing the HNC patients from healthy controls. Salivary microbial profiles and HNC symptoms may be potential biomarkers for HNC screening.
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Affiliation(s)
- Hao-Jiang Zuo
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
- West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Mei R. Fu
- Boston College William F. Connell School of Nursing, Chestnut Hill, MA, United States
| | - Hui-Ling Zhao
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Xin-Wen Du
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Zi-Yi Hu
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Xun-Ying Zhao
- West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xiao-Qin Ji
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Xian-Qiong Feng
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Wuerken Zhumajiang
- West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu, China
- Medical Statistics and Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Ting-Hui Zhou
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ya-Li Tian
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Xiao-Fang Pei
- West China School of Public Health/West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Rong Yu
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
| | - Xiu-Ying Hu
- West China Hospital/West China School of Nursing, Sichuan University, Chengdu, China
- Innovation Center of Nursing Research, West China School of Medicine/West China Hospital, Sichuan University, Chengdu, China
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332
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The Diversity, Composition, and Putative Functions of Gill-Associated Bacteria of Bathymodiolin Mussel and Vesicomyid Clam from Haima Cold Seep, South China Sea. Microorganisms 2020; 8:microorganisms8111699. [PMID: 33143295 PMCID: PMC7694083 DOI: 10.3390/microorganisms8111699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023] Open
Abstract
The Haima cold seep, which is one of the two active cold seeps in the South China Sea, is known for its great ecological importance. The seep bivalves are assumed to depend mainly on their bacterial symbiosis for survival and growth. However, information on the bacterial diversity, composition, and putative function of gill-associated of dominant dwelling animals in Haima cold seep remain elusive. Herein, we adopted a high-throughput sequencing of 16S rRNA gene amplicons, and function prediction methods (Functional Annotation of Prokaryotic Taxa (FAPROTAX) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICURUSTs)) to purposely illustrate the taxonomic and phylogenetic diversity, composition, and putative functions of the symbionts in bathymodiolin mussel Gigantidas haimaensis (Bivalvia: Mytilidae: Gigantidas) and vesicomyid clam Archivesica marissinica (Bivalvia: Glossoidea: Vesicomyidae). The predominant microbes of both species were Proteobacteria and Gammaproteobacteria on the phylum and class level, respectively. The taxonomic and phylogenetic diversity of gill microbial communities in G. haimaensis were significantly different from those in A. marissinica (p < 0.05). Nine functional groups, including seven carbon-related biogeochemical groups, were identified through the FAPROTAX analysis. However, the most dominant groups for G. haimaensis and A. marissinica were both chemoheterotrophic. G. haimaensis and A. marissinica shared many pathways, however, 16 obtained Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologous groups (42.11%) significantly differed between the two species (p < 0.05). These findings would provide insight into the functions of microbes in the element cycling and energy flow as well as the host-symbiont relationship of bivalves in the Haima cold seep environment.
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333
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Pittman QJ. A gut feeling about the ketogenic diet in epilepsy. Epilepsy Res 2020; 166:106409. [DOI: 10.1016/j.eplepsyres.2020.106409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/22/2020] [Accepted: 06/27/2020] [Indexed: 02/08/2023]
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