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Li Y, Qiao X, Feng Y, Zhou R, Zhang K, Pan Y, Yan T, Yan L, Yang S, Wei X, Li P, Xu C, Lv Z, Tian Z. Characterization of the gut microbiota and fecal metabolome in the osteosarcoma mouse model. Aging (Albany NY) 2024; 16:205951. [PMID: 38967635 DOI: 10.18632/aging.205951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/21/2024] [Indexed: 07/06/2024]
Abstract
Previous studies have reported the correlation between gut microbiota (GM), GM-derived metabolites, and various intestinal and extra-intestinal cancers. However, limited studies have investigated the correlation between GM, GM-derived metabolites, and osteosarcoma (OS). This study successfully established a female BALB/c nude mouse model of OS. Mice (n = 14) were divided into the following two groups (n = 7/group): OS group named OG, injected with Saos-2 OS cells; normal control group named NCG, injected with Matrigel. The GM composition and metabolites were characterized using 16S rDNA sequencing and untargeted metabolomics, respectively. Bioinformatics analysis revealed that amino acid metabolism was dysregulated in OS. The abundances of bone metabolism-related genera Alloprevotella, Rikenellaceae_RC9_gut_group, and Muribaculum were correlated with amino acid metabolism, especially histidine metabolism. These findings suggest the correlation between GM, GM-derived metabolites, and OS pathogenesis. Clinical significance: The currently used standard therapeutic strategies for OS, including surgery, chemotherapy, and radiation, are not efficacious. The findings of this study provided novel insights for developing therapeutic, diagnostic, and prognostic strategies for OS.
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Affiliation(s)
- Yuan Li
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Xiaochen Qiao
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Yi Feng
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Ruhao Zhou
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Kun Zhang
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Yongchun Pan
- Department of Orthopedics, Third People's Hospital of Datong City, Datong 037006, Shanxi, P.R. China
| | - Ting Yan
- Translational Medicine Center, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
| | - Lei Yan
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Sen Yang
- Department of Orthopedics, The Second People's Hospital of Changzhi, Changzhi 046000, Shanxi, P.R. China
| | - Xiaochun Wei
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Pengcui Li
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Chaojian Xu
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Zhi Lv
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
| | - Zhi Tian
- Second Clinical Medical College, Shanxi Medical University, Taiyuan 030001, Shanxi, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan 030001, Shanxi, P.R. China
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Brame JE, Warbrick I, Heke D, Liddicoat C, Breed MF. Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort. ENVIRONMENTAL RESEARCH 2024; 252:118814. [PMID: 38555095 DOI: 10.1016/j.envres.2024.118814] [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: 01/17/2024] [Revised: 03/14/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.
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Affiliation(s)
- Joel E Brame
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Isaac Warbrick
- Taupua Waiora Māori Research Centre, Auckland University of Technology, Auckland, New Zealand.
| | - Deborah Heke
- Taupua Waiora Māori Research Centre, Auckland University of Technology, Auckland, New Zealand.
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
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3
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Finnegan PM, Garber PA, McKenney AC, Bicca-Marques JC, De la Fuente MF, Abreu F, Souto A, Schiel N, Amato KR, Mallott EK. Group membership, not diet, structures the composition and functional potential of the gut microbiome in a wild primate. mSphere 2024:e0023324. [PMID: 38940510 DOI: 10.1128/msphere.00233-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024] Open
Abstract
The gut microbiome has the potential to buffer temporal variations in resource availability and consumption, which may play a key role in the ability of animals to adapt to a broad range of habitats. We investigated the temporal composition and function of the gut microbiomes of wild common marmosets (Callithrix jacchus) exploiting a hot, dry environment-Caatinga-in northeastern Brazil. We collected fecal samples during two time periods (July-August and February-March) for 2 years from marmosets belonging to eight social groups. We used 16S rRNA gene amplicon sequencing, metagenomic sequencing, and butyrate RT-qPCR to assess changes in the composition and potential function of their gut microbiomes. Additionally, we identified the plant, invertebrate, and vertebrate components of the marmosets' diet via DNA metabarcoding. Invertebrate, but not plant or vertebrate, consumption varied across the year. However, gut microbiome composition and potential function did not markedly vary across study periods or as a function of diet composition. Instead, the gut microbiome differed markedly in both composition and potential function across marmosets residing in different social groups. We highlight the likely role of factors, such as behavior, residence, and environmental heterogeneity, in modulating the structure of the gut microbiome. IMPORTANCE In a highly socially cohesive and cooperative primate, group membership more strongly predicts gut microbiome composition and function than diet.
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Affiliation(s)
- Peter M Finnegan
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Paul A Garber
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- International Centre of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, China
| | - Anna C McKenney
- Department of Natural Sciences, Parkland College, Champaign, Illinois, USA
| | - Júlio César Bicca-Marques
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católicado Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Filipa Abreu
- Comparative BioCognition, Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
| | - Antonio Souto
- Department of Zoology, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Nicola Schiel
- Laboratório de Etologia Teórica e Aplicada, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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Abbasi E, Akçay E. Host control and species interactions jointly determine microbiome community structure. Theor Popul Biol 2024; 158:185-194. [PMID: 38925487 DOI: 10.1016/j.tpb.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community. How the host immune response interacts with the within-microbiome community dynamics to affect the assembly of the microbiome has been largely unexplored. We present here a mathematical framework to elucidate the role of host immune response and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community density are most susceptible to changes in immune control and become invasion prone as host immune control strength is increased. Whereas highly competitive communities remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress the need to incorporate the role of host-control mechanisms to better understand microbiome community assembly and stability.
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Affiliation(s)
- Eeman Abbasi
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA.
| | - Erol Akçay
- Department of Biology, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104, USA
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5
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Hazra R, Chattopadhyay S, Mallick A, Gayen S, Roy S. Revealing the therapeutic properties of gut microbiota: transforming cancer immunotherapy from basic to clinical approaches. Med Oncol 2024; 41:175. [PMID: 38874788 DOI: 10.1007/s12032-024-02416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/25/2024] [Indexed: 06/15/2024]
Abstract
The immune system plays a pivotal role in the battle against cancer, serving as a formidable guardian in the ongoing fight against malignant cells. To combat these malignant cells, immunotherapy has emerged as a prevalent approach leveraging antibodies and peptides such as anti-PD-1, anti-PD-L1, and anti-CTLA-4 to inhibit immune checkpoints and activate T lymphocytes. The optimization of gut microbiota plays a significant role in modulating the defense system in the body. This study explores the potential of certain gut-resident bacteria to amplify the impact of immunotherapy. Contemporary antibiotic treatments, which can impair gut flora, may diminish the efficacy of immune checkpoint blockers. Conversely, probiotics or fecal microbiota transplantation can help re-establish intestinal microflora equilibrium. Additionally, the gut microbiome has been implicated in various strategies to counteract immune resistance, thereby enhancing the success of cancer immunotherapy. This paper also acknowledges cutting-edge technologies such as nanotechnology, CAR-T therapy, ACT therapy, and oncolytic viruses in modulating gut microbiota. Thus, an exhaustive review of literature was performed to uncover the elusive link that could potentiate the gut microbiome's role in augmenting the success of cancer immunotherapy.
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Affiliation(s)
- Rudradeep Hazra
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Soumyadeep Chattopadhyay
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Arijit Mallick
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Sakuntala Gayen
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India
| | - Souvik Roy
- Department of Pharmaceutical Technology, Kolkata-Group of Institutions, NSHM Knowledge Campus, 124, B. L. Saha Road, Tara Park, Behala, Kolkata, West Bengal, 700053, India.
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Ji G, Zhao J, Si X, Song W. Targeting bacterial metabolites in tumor for cancer therapy: An alternative approach for targeting tumor-associated bacteria. Adv Drug Deliv Rev 2024; 211:115345. [PMID: 38834140 DOI: 10.1016/j.addr.2024.115345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/11/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024]
Abstract
Emerging evidence reveal that tumor-associated bacteria (TAB) can facilitate the initiation and progression of multiple types of cancer. Recent work has emphasized the significant role of intestinal microbiota, particularly bacteria, plays in affecting responses to chemo- and immuno-therapies. Hence, it seems feasible to improve cancer treatment outcomes by targeting intestinal bacteria. While considering variable richness of the intestinal microbiota and diverse components among individuals, direct manipulating the gut microbiota is complicated in clinic. Tumor initiation and progression requires the gut microbiota-derived metabolites to contact and reprogram neoplastic cells. Hence, directly targeting tumor-associated bacteria metabolites may have the potential to provide alternative and innovative strategies to bypass the gut microbiota for cancer therapy. As such, there are great opportunities to explore holistic approaches that incorporates TAB-derived metabolites and related metabolic signals modulation for cancer therapy. In this review, we will focus on key opportunistic areas by targeting TAB-derived metabolites and related metabolic signals, but not bacteria itself, for cancer treatment, and elucidate future challenges that need to be addressed in this emerging field.
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Affiliation(s)
- Guofeng Ji
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jingjing Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang 453100, China
| | - Xinghui Si
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Biomedical Polymers Engineering Laboratory, Changchun 130022, China
| | - Wantong Song
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China; Jilin Biomedical Polymers Engineering Laboratory, Changchun 130022, China.
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Herlemann DPR, Tammert H, Kivistik C, Käiro K, Kisand V. Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water. Microbiologyopen 2024; 13:e13. [PMID: 38825966 PMCID: PMC11144953 DOI: 10.1002/mbo3.1413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 06/04/2024] Open
Abstract
The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.
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Affiliation(s)
- Daniel P. R. Herlemann
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Department of Biological OceanographyLeibniz Institute for Baltic Sea Research Warnemünde (IOW)RostockGermany
| | - Helen Tammert
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
| | - Carmen Kivistik
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Kairi Käiro
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
| | - Veljo Kisand
- Centre for Limnology, Institute of Agricultural and Environmental SciencesEstonian University of Life SciencesTartu CountyEstonia
- Institute of TechnologyUniversity of TartuTartuEstonia
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Yonatan Y, Kahn S, Bashan A. Interactions-based classification of a single microbial sample. CELL REPORTS METHODS 2024; 4:100775. [PMID: 38744286 PMCID: PMC11133833 DOI: 10.1016/j.crmeth.2024.100775] [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: 06/14/2023] [Revised: 02/11/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based on the interspecific microbial relationships. We verify, using both numerical simulations as well as real and shuffled microbial profiles from the human oral cavity, that the method can classify single samples based on their interspecific interactions. By analyzing the gut microbiome of people with autistic spectrum disorder, we found that our interaction-based method can improve the classification of individual subjects based on a single microbial sample. These results demonstrate that the underlying ecological interactions can be practically utilized to facilitate microbiome-based diagnosis and precision medicine.
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Affiliation(s)
- Yogev Yonatan
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel
| | - Shaya Kahn
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel
| | - Amir Bashan
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel.
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Ludington WB. The importance of host physical niches for the stability of gut microbiome composition. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230066. [PMID: 38497267 PMCID: PMC10945397 DOI: 10.1098/rstb.2023.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/04/2023] [Indexed: 03/19/2024] Open
Abstract
Gut bacteria are prevalent throughout the Metazoa and form complex microbial communities associated with food breakdown, nutrient provision and disease prevention. How hosts acquire and maintain a consistent bacterial flora remains mysterious even in the best-studied animals, including humans, mice, fishes, squid, bugs, worms and flies. This essay visits the evidence that hosts have co-evolved relationships with specific bacteria and that some of these relationships are supported by specialized physical niches that select, sequester and maintain microbial symbionts. Genetics approaches could uncover the mechanisms for recruiting and maintaining the stable and consistent members of the microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- William B. Ludington
- Department of Biosphere Sciences and Engineering, Carnegie Institution for Science, Baltimore, MD 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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Ma ZS, Shi P. Critical complex network structures in animal gastrointestinal tract microbiomes. Anim Microbiome 2024; 6:23. [PMID: 38702785 PMCID: PMC11067214 DOI: 10.1186/s42523-024-00291-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/21/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Living things from microbes to their hosts (plants, animals and humans) interact with each other, and their relationships may be described with complex network models. The present study focuses on the critical network structures, specifically the core/periphery nodes and backbones (paths of high-salience skeletons) in animal gastrointestinal microbiomes (AGMs) networks. The core/periphery network (CPN) mirrors nearly ubiquitous nestedness in ecological communities, particularly dividing the network as densely interconnected core-species and periphery-species that only sparsely linked to the core. Complementarily, the high-salience skeleton network (HSN) mirrors the pervasive asymmetrical species interactions (strictly microbial species correlations), particularly forming heterogenous pathways in AGM networks with both "backbones" and "rural roads" (regular or weak links). While the cores and backbones can act as critical functional structures, the periphery nodes and weak links may stabilize network functionalities through redundancy. RESULTS Here, we build and analyze 36 pairs of CPN/HSN for the AGMs based on 4903 gastrointestinal-microbiome samples containing 473,359 microbial species collected from 318 animal species covering all vertebrate and four major invertebrate classes. The network analyses were performed at host species, order, class, phylum, kingdom scales and diet types with selected and comparative taxon pairs. Besides diet types, the influence of host phylogeny, measured with phylogenetic (evolutionary) timeline or "age", were integrated into the analyses. For example, it was found that the evolutionary trends of three primary microbial phyla (Bacteroidetes/Firmicutes/Proteobacteria) and their pairwise abundance-ratios in animals do not mirror the patterns in modern humans phylogenetically, although they are consistent in terms of diet types. CONCLUSIONS Overall, the critical network structures of AGMs are qualitatively and structurally similar to those of the human gut microbiomes. Nevertheless, it appears that the critical composition (the three phyla of Bacteroidetes, Firmicutes, and Proteobacteria) in human gut microbiomes has broken the evolutionary trend from animals to humans, possibly attributable to the Anthropocene epoch and reflecting the far-reaching influences of agriculture and industrial revolution on the human gut microbiomes. The influences may have led to the deviations between modern humans and our hunter-gather ancestors and animals.
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Affiliation(s)
- Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
- Faculty of Arts and Science, Harvard Forest, Harvard University, Cambridge, MA, 02138, USA.
| | - Peng Shi
- Evolutionary and Functional Genomics Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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11
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Raulo A, Bürkner PC, Finerty GE, Dale J, Hanski E, English HM, Lamberth C, Firth JA, Coulson T, Knowles SCL. Social and environmental transmission spread different sets of gut microbes in wild mice. Nat Ecol Evol 2024; 8:972-985. [PMID: 38689017 DOI: 10.1038/s41559-024-02381-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/01/2024] [Indexed: 05/02/2024]
Abstract
Gut microbes shape many aspects of organismal biology, yet how these key bacteria transmit among hosts in natural populations remains poorly understood. Recent work in mammals has emphasized either transmission through social contacts or indirect transmission through environmental contact, but the relative importance of different routes has not been directly assessed. Here we used a novel radio-frequency identification-based tracking system to collect long-term high-resolution data on social relationships, space use and microhabitat in a wild population of mice (Apodemus sylvaticus), while regularly characterizing their gut microbiota with 16S ribosomal RNA profiling. Through probabilistic modelling of the resulting data, we identify positive and statistically distinct signals of social and environmental transmission, captured by social networks and overlap in home ranges, respectively. Strikingly, microorganisms with distinct biological attributes drove these different transmission signals. While the social network effect on microbiota was driven by anaerobic bacteria, the effect of shared space was most influenced by aerotolerant spore-forming bacteria. These findings support the prediction that social contact is important for the transfer of microorganisms with low oxygen tolerance, while those that can tolerate oxygen or form spores may be able to transmit indirectly through the environment. Overall, these results suggest social and environmental transmission routes can spread biologically distinct members of the mammalian gut microbiota.
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Affiliation(s)
- Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Computing, University of Turku, Turku, Finland.
| | | | - Genevieve E Finerty
- Department of Biology, University of Oxford, Oxford, UK
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behaviour, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Jarrah Dale
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Holly M English
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Curt Lamberth
- Department of Biology, University of Oxford, Oxford, UK
| | - Josh A Firth
- Department of Biology, University of Oxford, Oxford, UK
- School of Biology, University of Leeds, Leeds, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
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12
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Omondi ZN, Caner A, Arserim SK. Trypanosomes and Gut Microbiota Interactions in Triatomine bugs and Tsetse Flies: A vectorial perspective. MEDICAL AND VETERINARY ENTOMOLOGY 2024. [PMID: 38651684 DOI: 10.1111/mve.12723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
Triatomines (kissing bugs) and tsetse flies (genus: Glossina) are natural vectors of Trypanosoma cruzi and Trypanosoma brucei, respectively. T. cruzi is the causative agent of Chagas disease, endemic in Latin America, while T. brucei causes African sleeping sickness disease in sub-Saharan Africa. Both triatomines and tsetse flies are host to a diverse community of gut microbiota that co-exist with the parasites in the gut. Evidence has shown that the gut microbiota of both vectors plays a key role in parasite development and transmission. However, knowledge on the mechanism involved in parasite-microbiota interaction remains limited and scanty. Here, we attempt to analyse Trypanosoma spp. and gut microbiota interactions in tsetse flies and triatomines, with a focus on understanding the possible mechanisms involved by reviewing published articles on the subject. We report that interactions between Trypanosoma spp. and gut microbiota can be both direct and indirect. In direct interactions, the gut microbiota directly affects the parasite via the formation of biofilms and the production of anti-parasitic molecules, while on the other hand, Trypanosoma spp. produces antimicrobial proteins to regulate gut microbiota of the vector. In indirect interactions, the parasite and gut bacteria affect each other through host vector-activated processes such as immunity and metabolism. Although we are beginning to understand how gut microbiota interacts with the Trypanosoma parasites, there is still a need for further studies on functional role of gut microbiota in parasite development to maximize the use of symbiotic bacteria in vector and parasite control.
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Affiliation(s)
- Zeph Nelson Omondi
- Department of Biology, Faculty of Science, Ege University, Izmir, Turkey
| | - Ayşe Caner
- Department of Parasitology, Faculty of Medicine, Ege University, Izmir, Turkey
- Department of Basic Oncology, Institute of Health Sciences, Ege University, Izmir, Turkey
| | - Suha Kenan Arserim
- Vocational School of Health Sciences, Manisa Celal Bayar University, Manisa, Turkey
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13
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Zhang K, Paul K, Jacobs JP, Cockburn MG, Bronstein JM, Del Rosario I, Ritz B. Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study. Environ Health 2024; 23:41. [PMID: 38627687 PMCID: PMC11020204 DOI: 10.1186/s12940-024-01078-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans. METHODS We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders. RESULTS OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6. CONCLUSION In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.
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Affiliation(s)
- Keren Zhang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Kimberly Paul
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Myles G Cockburn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeff M Bronstein
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA.
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14
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Druzhinin VG, Baranova ED, Demenkov PS, Matskova LV, Larionov AV. Composition of the sputum bacterial microbiome of patients with different pathomorphological forms of non-small-cell lung cancer. Vavilovskii Zhurnal Genet Selektsii 2024; 28:204-214. [PMID: 38680177 PMCID: PMC11043513 DOI: 10.18699/vjgb-24-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 05/01/2024] Open
Abstract
Recent studies have shown that the bacterial microbiome of the respiratory tract influences the development of lung cancer. Changes in the composition of the microbiome are observed in patients with chronic inflammatory processes. Such microbiome changes may include the occurrence of bacteria that cause oxidative stress and that are capable of causing genome damage in the cells of the host organism directly and indirectly. To date, the composition of the respiratory microbiome in patients with various histological variants of lung cancer has not been studied. In the present study, we determined the taxonomic composition of the sputum microbiome of 52 patients with squamous cell carcinoma of the lung, 52 patients with lung adenocarcinoma and 52 healthy control donors, using next-generation sequencing (NGS) on the V3-V4 region of the bacterial gene encoding 16S rRNA. The sputum microbiomes of patients with different histological types of lung cancer and controls did not show significant differences in terms of the species richness index (Shannon); however, the patients differed from the controls in terms of evenness index (Pielou). The structures of bacterial communities (beta diversity) in the adenocarcinoma and squamous cell carcinoma groups were also similar; however, when analyzed according to the matrix constructed by the Bray-Curtis method, there were differences between patients with squamous cell carcinoma and healthy subjects, but not between those with adenocarcinoma and controls. Using the LEFse method it was possible to identify an increase in the content of Bacillota (Streptococcus and Bacillus) and Actinomycetota (Rothia) in the sputum of patients with squamous cell carcinoma when compared with samples from patients with adenocarcinoma. There were no differences in the content of bacteria between the samples of patients with adenocarcinoma and the control ones. The content of representatives of the genera Streptococcus, Bacillus, Peptostreptococcus (phylum Bacillota), Prevotella, Macellibacteroides (phylum Bacteroidota), Rothia (phylum Actinomycetota) and Actinobacillus (phylum Pseudomonadota) was increased in the microbiome of sputum samples from patients with squamous cell carcinoma, compared with the control. Thus, the sputum bacterial microbiome of patients with different histological types of non-small-cell lung cancer has significant differences. Further research should be devoted to the search for microbiome biomarkers of lung cancer at the level of bacterial species using whole-genome sequencing.
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Affiliation(s)
- V G Druzhinin
- Kemerovo State University, Kemerovo, Russia Kemerovo State Medical University, Kemerovo, Russia
| | | | - P S Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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15
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Wu Y, Zhou T, Yang S, Yin B, Wu R, Wei W. Distinct Gut Microbial Enterotypes and Functional Dynamics in Wild Striped Field Mice ( Apodemus agrarius) across Diverse Populations. Microorganisms 2024; 12:671. [PMID: 38674615 PMCID: PMC11052172 DOI: 10.3390/microorganisms12040671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Rodents, including the striped field mouse (Apodemus agrarius), play vital roles in ecosystem functioning, with their gut microbiota contributing significantly to various ecological processes. Here, we investigated the structure and function of 94 wild A. agrarius individuals from 7 geographic populations (45°57' N, 126°48' E; 45°87' N, 126°37' E; 45°50' N, 125°31' E; 45°59' N, 124°37' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E), revealing two distinct enterotypes (Type1 and Type2) for the first time. Each enterotype showed unique microbial diversity, functions, and assembly processes. Firmicutes and Bacteroidetes dominated, with a significant presence of Lactobacillus and Muribaculaceae. Functional analysis highlighted metabolic differences, with Type1 emphasizing nutrient processing and Type2 showing higher energy production capacity. The analysis of the neutral model and the null model revealed a mix of stochastic (drift and homogenizing dispersal) and deterministic processes (homogenous selection) that shape the assembly of the microbiota, with subtle differences in the assembly processes between the two enterotypes. Correlation analysis showed that elevation and BMI were associated with the phylogenetic turnover of microbial communities, suggesting that variations in these factors may influence the composition and diversity of the gut microbiota in A. agrarius. Our study sheds light on gut microbial dynamics in wild A. agrarius populations, highlighting the importance of considering ecological and physiological factors in understanding host-microbiota interactions.
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Affiliation(s)
| | | | | | | | | | - Wanhong Wei
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (T.Z.); (S.Y.); (B.Y.); (R.W.)
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16
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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [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: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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17
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Ben Cheikh Y, Massol F, Giusti-Petrucciani N, Travers MA. Impact of epizootics on mussel farms: Insights into microbiota composition of Mytilus species. Microbiol Res 2024; 280:127593. [PMID: 38184970 DOI: 10.1016/j.micres.2023.127593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/05/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Outbreaks of marine mussel mortality on French farms could have different aetiologies. One of them implies Vibrio splendidus strains. Beyond the involvement of this pathogen, there is considerable evidence that diseases often result from interactions between several microbes and the host. In this study, we explored the bacterial communities associated with mussel species and the surrounding water collected from a mussel farm affected by mortalities. The microbiota of Mytilus edulis, Mytilus galloprovincialis and their hybrids displayed an abnormal abundance of Proteobacteria, in particular the genera Vibrio, Cobetia and Arcobacter. Despite the dysbiosis, the Mediterranean mussel showed a different microbiota profile with a higher richness and presence of the phylum Bacteroidetes. Bipartite network analyses at the level of bacteria families confirmed this finding and showed that the microbiomes of M. edulis and the hybrids tended to cluster together. In addition, injection of mussels with the virulent V. splendidus induced less mortality rate in M. galloprovincialis compared to the other Mytilus sp. suggesting a better resistance of the Mediterranean mussel to infection. Our findings point to a probable aetiology of pathobiome-mediated disease in mussels. To fully understand this phenomenon, more knowledge is needed on the roles of pathobiotic systems and their development during disease establishment.
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Affiliation(s)
- Yosra Ben Cheikh
- UMR-I 02 Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO), Université Le Havre Normandie, Cedex 76063 Le Havre, France.
| | - François Massol
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nathalie Giusti-Petrucciani
- UMR-I 02 Environmental Stresses and Biomonitoring of Aquatic Ecosystems (SEBIO), Université Le Havre Normandie, Cedex 76063 Le Havre, France
| | - Marie-Agnès Travers
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34090 Montpellier, France
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18
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Wei P, Han W, Zhang Z, Tian X, Yang C, Wang Q, Xie W, Liu Y, Gao Y, Chang H. Microbiota in colorectal cancer related to liver metastasis. Chin J Cancer Res 2024; 36:17-24. [PMID: 38455371 PMCID: PMC10915638 DOI: 10.21147/j.issn.1000-9604.2024.01.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
The prevalence of colorectal cancer (CRC) is increasing annually and metastasis is the principal cause of death in patients with CRC, with the liver being the most frequently affected site. Many studies have shown a strong interplay between the gut flora, particularly Fusobacterium nucleatum (F. nucleatum), Escherichia coli, and Bacteroides fragilis, and the development of gut tumors. Some strains can induce gut inflammation and produce toxins that directly harm gut epithelial cells, ultimately accelerating the onset and progression of CRC. However, little clinical evidence exists on the specific interplay between the gut microflora and colorectal cancer liver metastasis (CRLM). Some research showed the existence of viable F. nucleatum in distant metastasis of CRC. Subsequently, gut microbiota products, such as lipopolysaccharides, sodium butyrate, and protein cathepsin K, were also found to affect the development of CRC. This article summarizes the mechanism and research status of the interplay between gut microflora and CRLM, discusses the importance of gut microflora in the treatment of CRLM, and proposes a new approach to understanding the mechanism of CRLM and potential treatments for the microbiome. It is anticipated that the gut microbiota will be a formidable therapeutic and prophylactic tool for treating and preventing CRLM.
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Affiliation(s)
- Peijun Wei
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weiming Han
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zitong Zhang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xue Tian
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Chen Yang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qiaoxuan Wang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weihao Xie
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
- Department of Pediatric Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
| | - Ying Liu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yuanhong Gao
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Hui Chang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
- Guangdong Provincial Clinical Research Center for Cancer, Guangzhou 510060, China
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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19
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Brunner JD, Chia N. Metabolic model-based ecological modeling for probiotic design. eLife 2024; 13:e83690. [PMID: 38380900 PMCID: PMC10942782 DOI: 10.7554/elife.83690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/19/2024] [Indexed: 02/22/2024] Open
Abstract
The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter 'probiotic' treatments intended to alter the composition of the microbiome. Despite so much promise and commercial interest, the factors that contribute to the success or failure of microbiome-targeted treatments remain unclear. We investigate the biotic interactions that lead to successful engraftment of a novel bacterial strain introduced to the microbiome as in probiotic treatments. We use pairwise genome-scale metabolic modeling with a generalized resource allocation constraint to build a network of interactions between taxa that appear in an experimental engraftment study. We create induced sub-graphs using the taxa present in individual samples and assess the likelihood of invader engraftment based on network structure. To do so, we use a generalized Lotka-Volterra model, which we show has strong ability to predict if a particular invader or probiotic will successfully engraft into an individual's microbiome. Furthermore, we show that the mechanistic nature of the model is useful for revealing which microbe-microbe interactions potentially drive engraftment.
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Affiliation(s)
- James D Brunner
- Biosciences Division, Los Alamos National LaboratoryLos AlamosUnited States
- Center for Nonlinear Studies, Los Alamos National LaboratoryLos AlamosUnited States
| | - Nicholas Chia
- Data Science and Learning, Argonne National LaboratoryLemontUnited States
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20
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Xie W, Zhong YS, Li XJ, Kang YK, Peng QY, Ying HZ. Postbiotics in colorectal cancer: intervention mechanisms and perspectives. Front Microbiol 2024; 15:1360225. [PMID: 38450163 PMCID: PMC10914944 DOI: 10.3389/fmicb.2024.1360225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
Colorectal cancer (CRC) is a common malignancy affecting the gastrointestinal tract worldwide. The etiology and progression of CRC are related to factors such as environmental influences, dietary structure, and genetic susceptibility. Intestinal microbiota can influence the integrity of the intestinal mucosal barrier and modulate intestinal immunity by secreting various metabolites. Dysbiosis of the intestinal microbiota can affect the metabolites of the microbial, leading to the accumulation of toxic metabolites, which can trigger chronic inflammation or DNA damage and ultimately lead to cellular carcinogenesis and the development of CRC. Postbiotics are preparations of inanimate microorganisms or their components that are beneficial to the health of the host, with the main components including bacterial components (e.g., exopolysaccharides, teichoic acids, surface layer protein) and metabolites (e.g., short-chain fatty acids, tryptophan metabolite, bile acids, vitamins and enzymes). Compared with traditional probiotics, it has a more stable chemical structure and higher safety. In recent years, it has been demonstrated that postbiotics are involved in regulating intestinal microecology and improving the progression of CRC, which provides new ideas for the prevention and diagnosis of CRC. In this article, we review the changes in intestinal microbiota in different states of the gut and the mechanisms of anti-tumor activity of postbiotic-related components, and discuss the potential significance of postbiotics in the diagnosis and treatment of CRC. This reviews the changes and pathogenesis of intestinal microbiota in the development of CRC, and summarizes the relevant mechanisms of postbiotics in resisting the development of CRC in recent years, as well as the advantages and limitations of postbiotics in the treatment process of CRC.
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Affiliation(s)
| | | | | | | | | | - Hua-Zhong Ying
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, China
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21
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Tarracchini C, Milani C, Lugli GA, Mancabelli L, Turroni F, van Sinderen D, Ventura M. The infant gut microbiota as the cornerstone for future gastrointestinal health. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:93-119. [PMID: 38637108 DOI: 10.1016/bs.aambs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy.
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22
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Lee JE, Park JK, Do Y. Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog. PLoS One 2024; 19:e0298245. [PMID: 38363754 PMCID: PMC10871480 DOI: 10.1371/journal.pone.0298245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/21/2024] [Indexed: 02/18/2024] Open
Abstract
The gut microbiota maintains a deeply symbiotic relationship with host physiology, intricately engaging with both internal (endogenous) and external (exogenous) factors. Anurans, especially those in temperate regions, face the dual challenges of significant external influences like hibernation and complex internal variances tied to different life histories. In our research, we sought to determine whether different life stages (juvenile versus adult) of the Japanese wrinkled frog (Glandirana rugosa) lead to distinct shifts in gut bacterial communities during winter (hibernation) and its subsequent transition to spring. As hypothesized, we observed a more pronounced variability in the gut bacterial diversity and abundance in juvenile frogs compared to their adult counterparts. This suggests that the gut environment may be more resilient or stable in adult frogs during their hibernation period. However, this pronounced difference was confined to the winter season; by spring, the diversity and abundance of gut bacteria in both juvenile and adult frogs aligned closely. Specifically, the variance in gut bacterial diversity and composition between winter and spring appears to mirror the frogs' ecological adaptations. During the hibernation period, a dominance of Proteobacteria suggests an emphasis on supporting intracellular transport and maintaining homeostasis, as opposed to active metabolism in the frogs. Conversely, come spring, an uptick in bacterial diversity coupled with a dominance of Firmicutes and Bacteroidetes points to an upsurge in metabolic activity post-hibernation, favoring enhanced nutrient assimilation and energy metabolism. Our findings highlight that the relationship between the gut microbiome and its host is dynamic and bidirectional. However, the extent to which changes in gut bacterial diversity and composition contribute to enhancing hibernation physiology in frogs remains an open question, warranting further investigation.
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Affiliation(s)
- Ji-Eun Lee
- Department of Biological Sciences, Kongju National University, Gongju, Republic of Korea
| | - Jun-Kyu Park
- Department of Biological Sciences, Kongju National University, Gongju, Republic of Korea
| | - Yuno Do
- Department of Biological Sciences, Kongju National University, Gongju, Republic of Korea
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23
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Scholier T, Lavrinienko A, Kallio ER, Watts PC, Mappes T. Effects of past and present habitat on the gut microbiota of a wild rodent. Proc Biol Sci 2024; 291:20232531. [PMID: 38320610 PMCID: PMC10846943 DOI: 10.1098/rspb.2023.2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
The response of the gut microbiota to changes in the host environment can be influenced by both the host's past and present habitats. To quantify their contributions for two different life stages, we studied the gut microbiota of wild bank voles (Clethrionomys glareolus) by performing a reciprocal transfer experiment with adults and their newborn offspring between urban and rural forests in a boreal ecosystem. Here, we show that the post-transfer gut microbiota in adults did not shift to resemble the post-transfer gut microbiota of animals 'native' to the present habitat. Instead, their gut microbiota appear to be structured by both their past and present habitat, with some features of the adult gut microbiota still determined by the past living environment (e.g. alpha diversity, compositional turnover). By contrast, we did not find evidence of the maternal past habitat (maternal effects) affecting the post-transfer gut microbiota of the juvenile offspring, and only a weak effect of the present habitat. Our results show that both the contemporary living environment and the past environment of the host organism can structure the gut microbiota communities, especially in adult individuals. These data are relevant for decision-making in the field of conservation and wildlife translocations.
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Affiliation(s)
- Tiffany Scholier
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich 8092, Switzerland
| | - Eva R. Kallio
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Phillip C. Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
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Paiano L, Mastronardi M, Campisciano G, Rosso N, Casagranda B, Comar M, de Manzini N, Palmisano S. Liver Bacterial Colonization in Patients with Obesity and Gut Dysbiosis. Obes Surg 2024; 34:402-408. [PMID: 38102371 DOI: 10.1007/s11695-023-06989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
PURPOSE Recently, the link between gut microbiota, liver inflammation, and obesity has become an interesting focus of research. The aim of this study is to show the possible relation between gut microbiota dysbiosis in patients with obesity and the presence of bacterial genomes in their liver biopsies. MATERIALS AND METHODS A prospective study on patients undergoing bariatric surgery was carried out. Anthropometric and metabolic data, comorbidities, stool samples, and hepatic biopsies were collected and analyzed at the time of surgery. The V3-16S rRNA region was sequenced using the Ion Torrent new-generation sequencing platform. RESULTS In each of the 23 patients enrolled, the bacterial population was analyzed both in the stools and liver. In eight patients (34.7%), Prevotella (62.5%), Bacteroides (50%), Streptococcus (12.5%), and Dalister (12.5%) were found in both samples, simultaneously; in 15 cases, the liver was free from colonization. The statistically significant difference between groups was a Roseburia intestinalis reduction in fecal samples of patients with liver biopsies colonized by bacteria (1% vs 3%; p = 0.0339). CONCLUSION To the best of our knowledge, this is the first study reporting the presence of bacterial genome in a liver biopsy on bariatric patients, instead of the microbe-associated molecular patterns. Notably, in literature, the presence of Roseburia intestinalis in stool samples has been shown to prevent intestinal inflammation playing its role in the gut barrier integrity. In our population, the Roseburia reduction was associated with the presence of bacterial genome in the liver, probably related to a greater permeability of the gut and vascular barriers.
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Affiliation(s)
- Lucia Paiano
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
| | - Manuela Mastronardi
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy.
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy.
| | - Giuseppina Campisciano
- Institute for Maternal and Child Health IRCCS, Burlo Garofolo, Via dell' Istria 65/1, 34149, Trieste, Italy
| | - Natalia Rosso
- Fondazione Italiana Fegato, Centro Studi Fegato, Area Science Park Basovizza Bldg.Q SS14 Km, 163.5, 34149, Trieste, Italy
| | - Biagio Casagranda
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
| | - Manola Comar
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Institute for Maternal and Child Health IRCCS, Burlo Garofolo, Via dell' Istria 65/1, 34149, Trieste, Italy
| | - Nicolò de Manzini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
| | - Silvia Palmisano
- Department of Medical, Surgical and Health Sciences, University of Trieste, Strada di Fiume, 447, 34149, Trieste, Italy
- Surgical Clinic Unit, Cattinara Hospital, ASUGI, Strada di Fiume, 447, 34149, Trieste, Italy
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Zhu Y, Ma R, Hu L, Yang H, Gong H, He K. Structure, variation and assembly of body-wide microbiomes in endangered crested ibis Nipponia nippon. Mol Ecol 2024; 33:e17238. [PMID: 38108198 DOI: 10.1111/mec.17238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/17/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
Limited knowledge of bird microbiome in the all-body niche hinders our understanding of host-microbial relationships and animal health. Here, we characterized the microbial composition of the crested ibis from 13 body sites, representing the cloaca, oral, feather and skin habitats, and explored assembly mechanism structuring the bacterial community of the four habitats respectively. The bacterial community characteristics were distinct among the four habitats. The skin harboured the highest alpha diversity and most diverse functions, followed by feather, oral and cloaca. Individual-specific features were observed when the skin and feathers were concentrated independently. Skin and feather samples of multiple body sites from the same individual were more similar than those from different individuals. Although a significant proportion of the microbiota in the host (85.7%-96.5%) was not derived from the environmental microbiome, as body sites became more exposed to the environment, the relative importance of neutral processes (random drift or dispersal) increased. Neutral processes were the most important contributor in shaping the feather microbiome communities (R2 = .859). A higher percentage of taxa (29.3%) on the skin were selected by hosts compared to taxa on other body habitats. This study demonstrated that niche speciation and partial neutral processes, rather than environmental sources, contribute to microbiome variation in the crested ibis. These results enhance our knowledge of baseline microbial diversity in birds and will aid health management in crested ibises in the future.
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Affiliation(s)
- Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Provincial Key Laboratory for Alpine Grassland Conservation and Utilization on Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Ruifeng Ma
- Institute of Qinghai-Tibetan Plateau, Provincial Key Laboratory for Alpine Grassland Conservation and Utilization on Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Lei Hu
- Institute of Qinghai-Tibetan Plateau, Provincial Key Laboratory for Alpine Grassland Conservation and Utilization on Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Haiqiong Yang
- Emei Breeding Center for Crested Ibis, Emei, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Haizhou Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
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26
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Liu S, Imad S, Hussain S, Xiao S, Yu X, Cao H. Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs. BMC Microbiol 2024; 24:34. [PMID: 38262927 PMCID: PMC10804495 DOI: 10.1186/s12866-023-03150-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Frogs are critical economic animals essential to agricultural ecosystem equilibrium. However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings. While frog-associated microbiota contribute to elemental cycling and immunity, the effects of frog sex and health on gut bacteria remain understudied, and the relationship between frog habitat and soil microbes is unclear. We aimed to determine how frog sex, health status and habitat influence symbiotic bacteria and community assembly mechanism to provide guidance for sustainable frog farming and conservation. RESULTS We employed 16S rRNA sequencing to investigate gut microbiota differences in relation to frog sex and health status. We also compared symbiotic communities in frog-aggregation, native and soybean soil on the farm. Results showed that gut bacterial β-diversity and taxonomy were markedly influenced by frog sex and health. Healthy frogs had more robust gut bacterial metabolism than frogs infected with MID. Cooccurrence network analysis revealed that healthy female frogs had more complex microbial network structure than males; however, diseased males showed the greatest network complexity. The assembly mechanism of gut bacteria in male frogs was dominated by deterministic processes, whereas in female frogs it was dominated by stochastic processes. Among symbiotic bacteria in frog habitat soils, deterministic processes predominantly shaped the community assembly of soybean soil. In particular, soybean soil was enriched in pathogens and nitrogen functions, whereas frog-aggregation soil was markedly increased in sulphur respiration and hydrocarbon degradation. CONCLUSION Our study reveals that sex mainly alters the interaction network and assembly mechanism of frog intestinal bacteria; MID infection significantly inhibits the metabolic functions of intestinal bacteria. Furthermore, diverse frog habitat soils could shape more symbiotic bacteria to benefit frog farming. Our findings provide new horizons for symbiotic bacteria among frogs, which could contribute to sustainable agriculture and ecological balance.
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Affiliation(s)
- Senlin Liu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Sewar Imad
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Sarfraz Hussain
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | | | - Xiaowei Yu
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affair, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, Jiangsu, 210095, People's Republic of China.
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Clemente-Suárez VJ, Redondo-Flórez L, Rubio-Zarapuz A, Martín-Rodríguez A, Tornero-Aguilera JF. Microbiota Implications in Endocrine-Related Diseases: From Development to Novel Therapeutic Approaches. Biomedicines 2024; 12:221. [PMID: 38255326 PMCID: PMC10813640 DOI: 10.3390/biomedicines12010221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
This comprehensive review article delves into the critical role of the human microbiota in the development and management of endocrine-related diseases. We explore the complex interactions between the microbiota and the endocrine system, emphasizing the implications of microbiota dysbiosis for the onset and progression of various endocrine disorders. The review aims to synthesize current knowledge, highlighting recent advancements and the potential of novel therapeutic approaches targeting microbiota-endocrine interactions. Key topics include the impact of microbiota on hormone regulation, its role in endocrine pathologies, and the promising avenues of microbiota modulation through diet, probiotics, prebiotics, and fecal microbiota transplantation. We underscore the importance of this research in advancing personalized medicine, offering insights for more tailored and effective treatments for endocrine-related diseases.
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Affiliation(s)
- Vicente Javier Clemente-Suárez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain; (V.J.C.-S.); (A.R.-Z.); (J.F.T.-A.)
- Grupo de Investigación en Cultura, Educación y Sociedad, Universidad de la Costa, Barranquilla 080002, Colombia
| | - Laura Redondo-Flórez
- Department of Health Sciences, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, C/ Tajo s/n, 28670 Villaviciosa de Odón, Spain;
| | - Alejandro Rubio-Zarapuz
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain; (V.J.C.-S.); (A.R.-Z.); (J.F.T.-A.)
| | - Alexandra Martín-Rodríguez
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain; (V.J.C.-S.); (A.R.-Z.); (J.F.T.-A.)
| | - José Francisco Tornero-Aguilera
- Faculty of Sports Sciences, Universidad Europea de Madrid, Tajo Street, s/n, 28670 Madrid, Spain; (V.J.C.-S.); (A.R.-Z.); (J.F.T.-A.)
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Tian Z, Qiao X, Wang Z, Li X, Pan Y, Wei X, Lv Z, Li P, Du Q, Wei W, Yan L, Chen S, Xu C, Feng Y, Zhou R. Cisplatin and doxorubicin chemotherapy alters gut microbiota in a murine osteosarcoma model. Aging (Albany NY) 2024; 16:1336-1351. [PMID: 38231481 PMCID: PMC10866425 DOI: 10.18632/aging.205428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/01/2023] [Indexed: 01/18/2024]
Abstract
The gut microbiota is closely associated with tumor progression and treatment in a variety of cancers. However, the alteration of the gut microbiota during the progression and chemotherapy of osteosarcoma remains poorly understood. This study aimed to explore the relationship between dysbiosis in the gut microbiota during osteosarcoma growth and chemotherapy treatment. We used BALB/c nude mice to establish osteosarcoma xenograft tumor models and administered cisplatin (CDDP) or doxorubicin (DOX) intraperitonially once every 2 days for a total of 5 times to establish effective chemotherapy models. Fecal samples were collected and processed for 16S rRNA sequencing to analyze the composition of the gut microbiota. We observed that the abundances of Colidextribacter, Lachnospiraceae_NK4A136_group, Lachnospiraceae_UCG-010, Lachnospiraceae_UCG-006, and Lachnoclostridium decreased, and the abundances of Alloprevotella and Enterorhabdus increased in the osteosarcoma mouse model group compared to those in the control group. In addition, genera, such as Lachnoclostridium and Faecalibacterium were more abundant in chemotherapy-treated mice than those in saline-treated mice. Additionally, we observed that alterations in some genera, including Lachnoclostridium and Colidextribacter in the osteosarcoma animal model group returned to normal after CDDP or DOX treatment. Furthermore, the function of the gut microbiota was inferred through PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), which indicated that metabolism-related microbiota was highly enriched and significantly different in each group. These results indicate correlations between dysbiosis of the gut microbiota and osteosarcoma growth and chemotherapy treatment with CDDP or DOX and may provide novel avenues for the development of potential adjuvant therapies.
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Affiliation(s)
- Zhi Tian
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Xiaochen Qiao
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, JinZhong Hospital Affiliated to Shanxi Medical University, Jinzhong, Shanxi 030600, P.R. China
| | - Zhichao Wang
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan 030032, P.R. China
| | - Xiaoyan Li
- Shanxi Province Cancer Hospital, Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
| | - Yongchun Pan
- Department of Orthopedics, The Third People’s Hospital of Datong City, Datong, Shanxi 037006, P.R. China
| | - Xiaochun Wei
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Zhi Lv
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Pengcui Li
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Qiujing Du
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan 030032, P.R. China
| | - Wenhao Wei
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Lei Yan
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Song Chen
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Chaojian Xu
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Yi Feng
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
| | - Ruhao Zhou
- Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
- Department of Orthopedics, The Second Hospital of Shanxi Medical University, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Taiyuan, Shanxi 030001, P.R. China
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Barbour KM, Martiny JBH. Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system. THE ISME JOURNAL 2024; 18:wrae043. [PMID: 38506671 PMCID: PMC11008689 DOI: 10.1093/ismejo/wrae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 03/21/2024]
Abstract
Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.
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Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, United States
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30
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Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
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Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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McGuinness AJ, Stinson LF, Snelson M, Loughman A, Stringer A, Hannan AJ, Cowan CSM, Jama HA, Caparros-Martin JA, West ML, Wardill HR. From hype to hope: Considerations in conducting robust microbiome science. Brain Behav Immun 2024; 115:120-130. [PMID: 37806533 DOI: 10.1016/j.bbi.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/14/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome science has been one of the most exciting and rapidly evolving research fields in the past two decades. Breakthroughs in technologies including DNA sequencing have meant that the trillions of microbes (particularly bacteria) inhabiting human biological niches (particularly the gut) can be profiled and analysed in exquisite detail. This microbiome profiling has profound impacts across many fields of research, especially biomedical science, with implications for how we understand and ultimately treat a wide range of human disorders. However, like many great scientific frontiers in human history, the pioneering nature of microbiome research comes with a multitude of challenges and potential pitfalls. These include the reproducibility and robustness of microbiome science, especially in its applications to human health outcomes. In this article, we address the enormous promise of microbiome science and its many challenges, proposing constructive solutions to enhance the reproducibility and robustness of research in this nascent field. The optimisation of microbiome science spans research design, implementation and analysis, and we discuss specific aspects such as the importance of ecological principals and functionality, challenges with microbiome-modulating therapies and the consideration of confounding, alternative options for microbiome sequencing, and the potential of machine learning and computational science to advance the field. The power of microbiome science promises to revolutionise our understanding of many diseases and provide new approaches to prevention, early diagnosis, and treatment.
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Affiliation(s)
- Amelia J McGuinness
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Matthew Snelson
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia.
| | - Amy Loughman
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Andrea Stringer
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Australia
| | | | - Hamdi A Jama
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC, Australia
| | | | - Madeline L West
- Deakin University, Geelong, Australia, the Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine and Barwon Health, Geelong, Australia
| | - Hannah R Wardill
- Supportive Oncology Research Group, Precision Medicine (Cancer), South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide, Adelaide, South Australia, Australia
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Mazel F, Pitteloud C, Guisan A, Pellissier L. Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets. ISME COMMUNICATIONS 2024; 4:ycad013. [PMID: 38374896 PMCID: PMC10875604 DOI: 10.1093/ismeco/ycad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024]
Abstract
Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
| | - Camille Pitteloud
- Département de la mobilité, du territoire et de l'environnement, Service des forêts, de la nature et du paysage, Sion 1950, Switzerland
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne 1015, Switzerland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Department of Environmental Systems Science, ETH Zürich, Zürich 8092, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf 8903, Switzerland
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33
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Lyu R, Qu Y, Divaris K, Wu D. Methodological Considerations in Longitudinal Analyses of Microbiome Data: A Comprehensive Review. Genes (Basel) 2023; 15:51. [PMID: 38254941 PMCID: PMC11154524 DOI: 10.3390/genes15010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Biological processes underlying health and disease are inherently dynamic and are best understood when characterized in a time-informed manner. In this comprehensive review, we discuss challenges inherent in time-series microbiome data analyses and compare available approaches and methods to overcome them. Appropriate handling of longitudinal microbiome data can shed light on important roles, functions, patterns, and potential interactions between large numbers of microbial taxa or genes in the context of health, disease, or interventions. We present a comprehensive review and comparison of existing microbiome time-series analysis methods, for both preprocessing and downstream analyses, including differential analysis, clustering, network inference, and trait classification. We posit that the careful selection and appropriate utilization of computational tools for longitudinal microbiome analyses can help advance our understanding of the dynamic host-microbiome relationships that underlie health-maintaining homeostases, progressions to disease-promoting dysbioses, as well as phases of physiologic development like those encountered in childhood.
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Affiliation(s)
- Ruiqi Lyu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA;
| | - Yixiang Qu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Seppi M, Pasqualini J, Facchin S, Savarino EV, Suweis S. Emergent Functional Organization of Gut Microbiomes in Health and Diseases. Biomolecules 2023; 14:5. [PMID: 38275746 PMCID: PMC10813293 DOI: 10.3390/biom14010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.
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Affiliation(s)
- Marcello Seppi
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Jacopo Pasqualini
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Samir Suweis
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
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Härer A, Rennison DJ. The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals. mSphere 2023; 8:e0044223. [PMID: 38038446 PMCID: PMC10732045 DOI: 10.1128/msphere.00442-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of "replaying life's tape." Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.
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Affiliation(s)
- Andreas Härer
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
| | - Diana J. Rennison
- Department of Ecology, Behavior & Evolution, School of Biological Sciences , University of California San Diego, La Jolla, California, USA
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Jing M, Yang W, Ding X, Rao L, Zhang Q, Zhu J. Environmental heterogeneity associated with boat activity shapes bacteria and microeukaryotic communities with discrepant response patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166943. [PMID: 37690748 DOI: 10.1016/j.scitotenv.2023.166943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
With the development of global tourism, tourist boats, a significant form of anthropogenic disturbance, are having an increasingly serious impact on the structure and function of aquatic ecosystems. In this study, the effects of different intensities of tourist boat activities on the microbial communities of West lake, were investigated by high-throughput sequencing. The results showed significant differences in the composition of bacterioplankton and microeukaryotic communities between the high-intensity boat activity (HIBA) area and low-intensity boat activity (LIBA) area. Variation partitioning analysis showed that environmental factors contributed the most to microbial community variation, and the effect of boat activities on microbial communities mainly occurred through coupling with environmental factors. The contribution of boat activity to microbial community changes occupies the second place, the first being environmental factors. Co-occurrence network analyses showed that microbial communities in the HIBA area had more nodes and edges, higher connectivity and lower modularity than in the LIBA area, suggesting a more complex and stable network. Networks of associations between potential keystone taxa and environmental factors reveal the way in which boat activity affects microbial communities. The bacterial community responded strongly to environmental factors associated with boat activities, whereas the microeukaryotic community was more likely to be regulated by interspecific interactions. This also suggests that when faced with disturbances from the boat activity, microeukaryotes might exert a stronger direct resistance effect compared to bacterioplankton. These findings imply that bacterioplankton and microeukaryotes demonstrate distinct response patterns in the presence of disturbance caused by boat activity. Our research expand our understanding of the effects of boat activities on aquatic ecosystems and provide further insights into the assessment of anthropogenic disturbances in aquatic ecosystems.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, Ningbo 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, Ningbo 315800, China
| | - Xiuying Ding
- Hangzhou West Lake Administration, Hangzhou 310002, China
| | - Lihua Rao
- Hangzhou West Lake Administration, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, Ningbo 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo 315800, China.
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Hussein AA, Bhat TA, Jing Z, Gomez EC, Wasay MA, Singh PK, Liu S, Smith G, Guru KA. Does the urinary microbiome profile change after treatment of bladder cancer? World J Urol 2023; 41:3593-3598. [PMID: 37796319 DOI: 10.1007/s00345-023-04627-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
INTRODUCTION We sought to investigate the change in the urinary microbiome profile after transurethral resection of bladder tumor (TURBT). METHODS Urine specimens were collected from consecutive patients with bladder cancer. Patients were divided into those with bladder tumors ("Tumor group": de novo tumors or recurrent/progressed after TURBT ± intravesical therapy) versus those without evidence of recurrence after treatment "No Recurrent Tumor group". Samples were analyzed using 16S rRNA sequencing. Alteration in the urinary microbiome was described in terms of alpha (diversity within a sample measured by Observed, Chao, Shannon, and Simpson indices), beta diversities (diversity among different samples measured by Brady Curtis Diversity index), and differential abundance of bacteria at the genus level. Analyses were adjusted for gender, method of preservation (frozen vs preservative), and method of collection (mid-stream vs. catheter). RESULTS Sixty-eight samples were analyzed (42 in "Tumor" vs 26 in "No Recurrent Tumor" groups). The median age was 70 years (IQR 64-74) and 85% were males. All patients in the "No Recurrent Tumor" group had non-muscle invasive bladder cancer and 85% received BCG compared to 69% and 43% for the "Tumor" group, respectively. There was no significant difference in alpha diversity (p > 0.05). Beta diversity was significantly different (p = 0.04). Veillonella and Bifidobacterium were more abundant in the "Tumor" group (> 2FC, p = 0.0002), while Escherichia-Shigella (> 2FC, p = 0.0002) and Helococcus (> 2FC, p = 0.0008) were more abundant in the "No Recurrent Tumor" group. CONCLUSION Bladder cancer patients with no recurrence and/or progression exhibited a different urinary microbiome profile compared to those with tumors.
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Affiliation(s)
- Ahmed A Hussein
- Department of Urology, A.T.L.A.S (Applied Technology Laboratory for Advanced Surgery) Program, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA.
| | - Tariq A Bhat
- Department of Urology, A.T.L.A.S (Applied Technology Laboratory for Advanced Surgery) Program, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Zhe Jing
- Department of Urology, A.T.L.A.S (Applied Technology Laboratory for Advanced Surgery) Program, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Mahmood Abdul Wasay
- Department of Urology, A.T.L.A.S (Applied Technology Laboratory for Advanced Surgery) Program, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Prashant K Singh
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Gary Smith
- Department of Urology, A.T.L.A.S (Applied Technology Laboratory for Advanced Surgery) Program, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
| | - Khurshid A Guru
- Department of Urology, A.T.L.A.S (Applied Technology Laboratory for Advanced Surgery) Program, Roswell Park Comprehensive Cancer Center, Elm & Carlton St, Buffalo, NY, 14263, USA
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38
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Zhuang Z, Zhou P, Wang J, Lu X, Chen Y. The Characteristics, Mechanisms and Therapeutics: Exploring the Role of Gut Microbiota in Obesity. Diabetes Metab Syndr Obes 2023; 16:3691-3705. [PMID: 38028999 PMCID: PMC10674108 DOI: 10.2147/dmso.s432344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Presently, obesity has emerged as a significant global public health concern due to its escalating prevalence and incidence rates. The gut microbiota, being a crucial environmental factor, has emerged as a key player in the etiology of obesity. Nevertheless, the intricate and specific interactions between obesity and gut microbiota, along with the underlying mechanisms, remain incompletely understood. This review comprehensively summarizes the gut microbiota characteristics in obesity, the mechanisms by which it induces obesity, and explores targeted therapies centered on gut microbiota restoration.
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Affiliation(s)
- Zequn Zhuang
- Department of General Surgery, the Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Peng Zhou
- Department of General Surgery, the Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Jing Wang
- Jiangnan University Medical Center, Wuxi, People’s Republic of China
| | - Xiaojing Lu
- Department of General Surgery, the Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
| | - Yigang Chen
- Department of General Surgery, the Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, People’s Republic of China
- Jiangnan University Medical Center, Wuxi, People’s Republic of China
- Wuxi Clinical College, Nantong University, Wuxi, People’s Republic of China
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Lv Y, Chang L, Liu J, Chen Q, Jiang J, Zhu W. Why Bufo gargarizans tadpoles grow bigger in Pb-contaminated environments? The gut microbiota matter. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 267:115601. [PMID: 37890260 DOI: 10.1016/j.ecoenv.2023.115601] [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: 07/03/2023] [Revised: 09/20/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
The impacts of lead/Pb2+ on ecosystems have received widespread attention. Growth suppression is a major toxic effect of Pb compounds on aquatic animals, however, some studies have also reported their growth-promoting effects. These complex outcomes may be explained by anions that accompany Pb2+ or by the multiple toxic mechanisms/pathways of Pb2+. To examine these hypotheses, we tested how Bufo gargarizans tadpoles responded to Pb(NO3)2 (100 and 200 μg/L Pb2+) using transcriptomics and microbiomics, with NaNO3 and blank groups as controls. Tadpoles exposed to Pb(NO3)2 showed delayed development while increased somatic growth in a dose-dependent manner, which can be attributed to the effects of NO3- and Pb2+, respectively. Tadpole transcriptomics revealed that exposure to NO3- downregulated the MAPK pathway at transcriptional level, explaining the development-suppressing effect of NO3-; while Pb2+ upregulated the transcription of detoxification pathways (e.g., xenobiotics metabolism by cytochrome P450 and glutathione metabolism), indicating cellular stress and thus contradicting the growth advantage of Pb2+-exposed tadpoles. Pb2+ exposure changed the tadpole gut microbiota drastically, characterized by increased polysaccharides and carbohydrate utilization while decreased fatty acid and amino acid consumption according to microbial functional analysis. Similar gut microbial variations were observed in field-collected tadpoles from different Pb2+ environments. This metabolic shift in gut microbiota likely improved the overall food utilization efficiency and increased the allocation of fatty acids and amino acids to the host, explaining the growth advantage of Pb2+-exposed tadpoles. In summary, our results suggest multiple toxic pathways of Pb2+, and the gut microbiota may affect the pollution outcomes on animals.
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Affiliation(s)
- Yan Lv
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
| | - Liming Chang
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
| | - Jiongyu Liu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
| | - Qiheng Chen
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, China.
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Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Front Microbiol 2023; 14:1261137. [PMID: 38033594 PMCID: PMC10684785 DOI: 10.3389/fmicb.2023.1261137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Department of Ocean Science (OCES), The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Masato S. Abe
- Faculty of Culture and Information Science, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masato Yamamichi
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Alberto Canarini
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
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41
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Ochoa-Sánchez M, Acuña Gomez EP, Moreno L, Moraga CA, Gaete K, Eguiarte LE, Souza V. Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns. PeerJ 2023; 11:e16290. [PMID: 37933257 PMCID: PMC10625763 DOI: 10.7717/peerj.16290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lucila Moreno
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Claudio A. Moraga
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Katherine Gaete
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Valeria Souza
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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Raulo A, Rojas A, Kröger B, Laaksonen A, Orta CL, Nurmio S, Peltoniemi M, Lahti L, Žliobaitė I. What are patterns of rise and decline? ROYAL SOCIETY OPEN SCIENCE 2023; 10:230052. [PMID: 38026026 PMCID: PMC10646453 DOI: 10.1098/rsos.230052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
The notions of change, such as birth, death, growth, evolution and longevity, extend across reality, including biological, cultural and societal phenomena. Patterns of change describe how success and composition of every entity, from species to societies, vary across time. Languages develop into new languages, music and fashion continuously evolve, economies rise and decline, ecological and societal crises come and go. A common way to perceive and analyse change processes is through patterns of rise and decline, the ubiquitous, often distinctively unimodal trajectories describing life histories of various entities. These patterns come in different shapes and are measured according to varying definitions. Depending on how they are measured, patterns of rise and decline can reveal, emphasize, mask or obscure important dynamics in natural and cultural phenomena. Importantly, the variations of how dynamics are measured can be vast, making it impossible to directly compare patterns of rise and decline across fields of science. Standardized analysis of these patterns has the potential to uncover important but overlooked commonalities across natural phenomena and potentially help us catch the onset of dramatic shifts in entities' state, from catastrophic crashes in success to gradual emergence of new entities. We provide a framework for standardized recognizing, characterizing and comparing patterns of change by combining understanding of dynamics across fields of science. Our toolkit aims at enhancing understanding of the most general tendencies of change, through two complementary perspectives: dynamics of emergence and dynamics of success. We gather comparable cases and data from different research fields and summarize open research questions that can help us understand the universal principles, perception-biases and field-specific tendencies in patterns of rise and decline of entities in nature.
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Affiliation(s)
- Aura Raulo
- Department of Computing, University of Turku, Turku, Finland
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Alexis Rojas
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Antti Laaksonen
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Carlos Lamuela Orta
- Mobility Research Group, VTT Technical Research Centre of Finland, Espoo, Uusimaa, Finland
| | - Silva Nurmio
- Department of Languages, University of Helsinki, Helsinki, Finland
| | - Mirva Peltoniemi
- Department of Industrial Engineering and Management, Tampere University, 33014 Tampere, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Indrė Žliobaitė
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
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43
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Oyeyemi BF, Kaur US, Paramraj A, Chintamani, Tandon R, Kumar A, Bhavesh NS. Microbiome analysis of saliva from oral squamous cell carcinoma (OSCC) patients and tobacco abusers with potential biomarkers for oral cancer screening. Heliyon 2023; 9:e21773. [PMID: 38034672 PMCID: PMC10685184 DOI: 10.1016/j.heliyon.2023.e21773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer and accounts for about 95% of all head and neck cancers with high mortality, usually at a late stage. Dysbiosis in the oral microbiome can lead to chronic inflammatory responses and may predispose to the development and progression of OSCC. Tobacco abuse plays an essential role in oral microbiome dysregulation and OSCC pathogenesis. We used 16S rRNA gene amplicon next-generation sequencing to examine microbial signatures unique to saliva from OSCC patients, tobacco abusers (TA) and controls (n = 10 for each group) to elucidate oral microbiome changes associated with tobacco abuse and OSCC. Overall, the oral microbiome compositions of class Betaproteobacteria and Epsilonproteobacteria, order Neisseriales, Burkholderiales and Campylobacterales, family Burkholderiaceae and Campylobacteraceae and genera Campylobacter and Leptotrichia revealed significant differences among OSCC patients, TA and control. Our preliminary pilot study not only serves as a basis for future studies with large sample size but also gives an indication of microbiome-based potential non-invasive biomarkers for early screening and monitoring of oral carcinogenesis transition due to tobacco abuse.
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Affiliation(s)
- Bolaji Fatai Oyeyemi
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Science Technology, The Federal Polytechnic, P.M.B. 5351, Ado-Ekiti, Nigeria
| | - Urvinder S. Kaur
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Amit Paramraj
- Department of Surgery, Vardhman Mahavir Medical College (VMMC)-Safdarjung Hospital, New Delhi, 110058, India
| | - Chintamani
- Department of Surgery, Vardhman Mahavir Medical College (VMMC)-Safdarjung Hospital, New Delhi, 110058, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Abhinav Kumar
- Department of Surgery, Vardhman Mahavir Medical College (VMMC)-Safdarjung Hospital, New Delhi, 110058, India
- Division of Trauma Surgery and Critical Care, Department of Surgical Disciplines, Jai Prakash Narayan Apex Trauma Center, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Parizadeh M, Arrieta MC. The global human gut microbiome: genes, lifestyles, and diet. Trends Mol Med 2023; 29:789-801. [PMID: 37516570 DOI: 10.1016/j.molmed.2023.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/31/2023]
Abstract
A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.
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Affiliation(s)
- Mona Parizadeh
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada.
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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46
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Young GR, Nelson A, Stewart CJ, Smith DL. Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease. Curr Opin Microbiol 2023; 75:102379. [PMID: 37647765 DOI: 10.1016/j.mib.2023.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Abstract
Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.
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Affiliation(s)
- Gregory R Young
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Andrew Nelson
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | | | - Darren L Smith
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK.
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Pisaniello A, Handley KM, White WL, Angert ER, Boey JS, Clements KD. Host individual and gut location are more important in gut microbiota community composition than temporal variation in the marine herbivorous fish Kyphosus sydneyanus. BMC Microbiol 2023; 23:275. [PMID: 37773099 PMCID: PMC10540440 DOI: 10.1186/s12866-023-03025-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Gut microbiota play a key role in the nutrition of many marine herbivorous fishes through hindgut fermentation of seaweed. Gut microbiota composition in the herbivorous fish Kyphosus sydneyanus (family Kyphosidae) varies between individuals and gut sections, raising two questions: (i) is community composition stable over time, especially given seasonal shifts in storage metabolites of dietary brown algae, and (ii) what processes influence community assembly in the hindgut? RESULTS We examined variation in community composition in gut lumen and mucosa samples from three hindgut sections of K. sydneyanus collected at various time points in 2020 and 2021 from reefs near Great Barrier Island, New Zealand. 16S rRNA gene analysis was used to characterize microbial community composition, diversity and estimated density. Differences in community composition between gut sections remained relatively stable over time, with little evidence of temporal variation. Clostridia dominated the proximal hindgut sections and Bacteroidia the most distal section. Differences were detected in microbial composition between lumen and mucosa, especially at genus level. CONCLUSIONS High variation in community composition and estimated bacterial density among individual fish combined with low variation in community composition temporally suggests that initial community assembly involved environmental selection and random sampling/neutral effects. Community stability following colonisation could also be influenced by historical contingency, where early colonizing members of the community may have a selective advantage. The impact of temporal changes in the algae may be limited by the dynamics of substrate depletion along the gut following feeding, i.e. the depletion of storage metabolites in the proximal hindgut. Estimated bacterial density, showed that Bacteroidota has the highest density (copies/mL) in distal-most lumen section V, where SCFA concentrations are highest. Bacteroidota genera Alistipes and Rikenella may play important roles in the breakdown of seaweed into useful compounds for the fish host.
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Affiliation(s)
- Alessandro Pisaniello
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
| | - Kim M Handley
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - W Lindsey White
- School of Science, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand
| | - Esther R Angert
- Department of Microbiology, Cornell University, 123 Wing Drive, Ithaca, NY, 14853, USA
| | - Jian Sheng Boey
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Kendall D Clements
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.
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48
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Fine DH, Schreiner H. Oral microbial interactions from an ecological perspective: a narrative review. FRONTIERS IN ORAL HEALTH 2023; 4:1229118. [PMID: 37771470 PMCID: PMC10527376 DOI: 10.3389/froh.2023.1229118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
Landscape ecology is a relatively new field of study within the sub-specialty of ecology that considers time and space in addition to structure and function. Landscape ecology contends that both the configuration (spatial pattern) and the composition (organisms both at the macro and or micro level) of an ecology can change over time. The oral cavity is an ideal place to study landscape ecology because of the variety of landscapes, the dynamic nature of plaque biofilm development, and the easy access to biofilm material. This review is intended to provide some specific clinical examples of how landscape ecology can influence the understanding of oral diseases and act as a supplement to diagnosis and treatment. The purpose of this review is two-fold; (1) to illustrate how landscape ecology can be used to clarify the two most prominent microbiologically induced infections in the oral cavity, and (2) how studies of oral microbiology can be used to enhance the understanding of landscape ecology. The review will distinguish between "habitat" and "niche" in a landscape and extend the concept that a "patch", is the demarcating unit of a habitat within a landscape. The review will describe how; (1) an individual patch, defined by its shape, edges and internal components can have an influence on species within the patch, (2) spatial dynamics over time within a patch can lead to variations or diversities of species within that patch space, and (3) an unwelcoming environment can promote species extinction or departure/dispersion into a more favorable habitat. Understanding this dynamic in relationship to caries and periodontal disease is the focus of this review.
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Affiliation(s)
- Daniel H. Fine
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, United States
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Prajjwal P, Inban P, Natarajan B, Gadam S, Marsool MD, Tariq H, Paras P, Vora N, Al-Aish ST, Marsool AD, Amir Hussin O. Remyelination in multiple sclerosis, along with its immunology and association with gut dysbiosis, lifestyle, and environmental factors. Ann Med Surg (Lond) 2023; 85:4417-4424. [PMID: 37663721 PMCID: PMC10473370 DOI: 10.1097/ms9.0000000000001127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/22/2023] [Indexed: 09/05/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease that damages the myelin sheath around the axons of the central nervous system. While there are periods of inflammation and remyelination in MS, the latter can sometimes be insufficient and lead to the formation of lesions in the brain and spinal cord. Environmental factors such as vitamin D deficiency, viral or bacterial infections, tobacco smoking, and anxiety have been shown to play a role in the development of MS. Dysbiosis, where the composition of the microbiome changes, may also be involved in the pathogenesis of MS by affecting the gut's microbial population and negatively impacting the integrity of the epithelia. While the cause of MS remains unknown, genetic susceptibility, and immunological dysregulation are believed to play a key role in the development of the disease. Further research is needed to fully understand the complex interplay between genetic, environmental, and microbial factors in the pathogenesis of MS.
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Affiliation(s)
| | | | - Balaganesh Natarajan
- St. George’s University School of Medicine, University Centre Grenada, West Indies, Grenada
| | | | | | | | | | - Neel Vora
- BJ Medical College, Ahmedabad, India
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50
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Ecklu-Mensah G, Choo-Kang C, Maseng MG, Donato S, Bovet P, Viswanathan B, Bedu-Addo K, Plange-Rhule J, Oti Boateng P, Forrester TE, Williams M, Lambert EV, Rae D, Sinyanya N, Luke A, Layden BT, O'Keefe S, Gilbert JA, Dugas LR. Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study. Nat Commun 2023; 14:5160. [PMID: 37620311 PMCID: PMC10449869 DOI: 10.1038/s41467-023-40874-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
The relationship between microbiota, short chain fatty acids (SCFAs), and obesity remains enigmatic. We employ amplicon sequencing and targeted metabolomics in a large (n = 1904) African origin cohort from Ghana, South Africa, Jamaica, Seychelles, and the US. Microbiota diversity and fecal SCFAs are greatest in Ghanaians, and lowest in Americans, representing each end of the urbanization spectrum. Obesity is significantly associated with a reduction in SCFA concentration, microbial diversity, and SCFA synthesizing bacteria, with country of origin being the strongest explanatory factor. Diabetes, glucose state, hypertension, obesity, and sex can be accurately predicted from the global microbiota, but when analyzed at the level of country, predictive accuracy is only universally maintained for sex. Diabetes, glucose, and hypertension are only predictive in certain low-income countries. Our findings suggest that adiposity-related microbiota differences differ between low-to-middle-income compared to high-income countries. Further investigation is needed to determine the factors driving this association.
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Affiliation(s)
- Gertrude Ecklu-Mensah
- Department of Pediatrics, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Maria Gjerstad Maseng
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Dep. of Gastroenterology, Oslo University Hospital, Oslo, Norway
- Bio-Me, Oslo, Norway
| | - Sonya Donato
- Department of Pediatrics, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne University Hospital, Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | | | - Kweku Bedu-Addo
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacob Plange-Rhule
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Prince Oti Boateng
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Terrence E Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Marie Williams
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V Lambert
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Nandipha Sinyanya
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Brian T Layden
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Stephen O'Keefe
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jack A Gilbert
- Department of Pediatrics, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Lara R Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA.
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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