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Xiang Q, Yan X, Shi X, Huang Y, Li L, Zhong J, Xu T, Tang S, Shi W, Zhou K. Prolonged premature rupture of membranes with increased risk of infection is associated with gut accumulation of Pseudomonas from the environment. Comput Struct Biotechnol J 2024; 23:2851-2860. [PMID: 39100803 PMCID: PMC11296040 DOI: 10.1016/j.csbj.2024.07.007] [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: 03/14/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024] Open
Abstract
Background Preterm premature rupture of membranes (PPROM) contributes to over one-third of preterm births, and PPROM infants are more susceptible to infections. However, the risk factors remain poorly understood. We here aim to investigate the association of duration of premature rupture of membranes (PROM) and environmental microbiota with the gut microbiota and infection in PPROM infants. Methods Forty-six premature infants were recruited from two hospitals, and infant fecal and environmental samples were collected. 16 s rRNA sequencing was performed to analyze the fecal and environmental microbiome. Human inflammatory cytokines in cord vein plasma were measured. Results The gut microbiota composition of PPROM infants was different from that of non-PPROM infants, and the microbiome phenotypes were predicted to be associated with a higher risk of infection, further evidenced by the significantly increased levels of IL-6 and IL-8 in cord vein plasma of PPROM infants. The diversity of the gut microbiota in PPROM infants increased significantly as the duration of PROM excessed 12 h, and Pseudomonas contributed significantly to the dynamic changes. The Pseudomonas species in the gut of PPROM infants were highly homologous to those detected in the ward environment, suggesting that prolonged PROM is associated with horizontal transmission of environmental pathogens, leading to a higher risk of infection. Conclusions This study highlights that the duration of PROM is associated with the accumulation of environmental pathogens in the gut of PPROM infants, which is a risk factor for nosocomial infections. Improving environmental hygiene could be effective in optimizing the clinical care of PPROM infants.
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Affiliation(s)
- Quanhang Xiang
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Xudong Yan
- Department of Neonatal Intensive Care Unit, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China
| | - Xing Shi
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Yi’e Huang
- Department of Prevention and Healthcare, Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, Shenzhen 518020, China
| | - Lingfeng Li
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Jiacheng Zhong
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
| | - Shaohui Tang
- Department of Gastroenterology, the First Affiliated Hospital, Jinan University, Guangzhou 510632, China
| | - Wei Shi
- Department of Obstetrics, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen 518020, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the Second Clinical Medical College (Shenzhen People's Hospital), Jinan University ; The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen 518000, China
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Juang DS, Wightman WE, Lozano GL, Juang TD, Barkal LJ, Yu J, Garavito MF, Hurley A, Venturelli OS, Handelsman J, Beebe DJ. Microbial community interactions on a chip. Proc Natl Acad Sci U S A 2024; 121:e2403510121. [PMID: 39288179 DOI: 10.1073/pnas.2403510121] [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: 02/19/2024] [Accepted: 08/04/2024] [Indexed: 09/19/2024] Open
Abstract
Multispecies microbial communities drive most ecosystems on Earth. Chemical and biological interactions within these communities can affect the survival of individual members and the entire community. However, the prohibitively high number of possible interactions within a microbial community has made the characterization of factors that influence community development challenging. Here, we report a Microbial Community Interaction (µCI) device to advance the systematic study of chemical and biological interactions within a microbial community. The µCI creates a combinatorial landscape made up of an array of triangular wells interconnected with circular wells, which each contains either a different chemical or microbial strain, generating chemical gradients and revealing biological interactions. Bacillus cereus UW85 containing green fluorescent protein provided the "target" readout in the triangular wells, and antibiotics or microorganisms in adjacent circular wells are designated the "variables." The µCI device revealed that gentamicin and vancomycin are antagonistic to each other in inhibiting the target B. cereus UW85, displaying weaker inhibitory activity when used in combination than alone. We identified three-member communities constructed with isolates from the plant rhizosphere that increased or decreased the growth of B. cereus. The µCI device enables both strain-level and community-level insight. The scalable geometric design of the µCI device enables experiments with high combinatorial efficiency, thereby providing a simple, scalable platform for systematic interrogation of three-factor interactions that influence microorganisms in solitary or community life.
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Affiliation(s)
- Duane S Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Wren E Wightman
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Gabriel L Lozano
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Terry D Juang
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Layla J Barkal
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Jiaquan Yu
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Manuel F Garavito
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Amanda Hurley
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Jo Handelsman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706
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Chen JZ, Junker A, Zheng I, Gerardo NM, Vega NM. A strong priority effect in the assembly of a specialized insect-microbe symbiosis. Appl Environ Microbiol 2024:e0081824. [PMID: 39291984 DOI: 10.1128/aem.00818-24] [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: 04/25/2024] [Accepted: 08/18/2024] [Indexed: 09/19/2024] Open
Abstract
Specialized host-microbe symbioses are ecological communities, whose composition is shaped by various processes. Microbial community assembly in these symbioses is determined in part by interactions between taxa that colonize ecological niches available within habitat patches. The outcomes of these interactions, and by extension the trajectory of community assembly, can display priority effects-dependency on the order in which taxa first occupy these niches. The underlying mechanisms of these phenomena vary from system to system and are often not well resolved. Here, we characterize priority effects in colonization of the squash bug (Anasa tristis) by bacterial symbionts from the genus Caballeronia, using pairs of strains that are known to strongly compete during host colonization, as well as strains that are isogenic and thus functionally identical. By introducing symbiont strains into individual bugs in a sequential manner, we show that within-host populations established by the first colonist are extremely resistant to invasion, regardless of strain identity and competitive interactions. By knocking down the population of an initial colonist with antibiotics, we further show that colonization success by the second symbiont is still diminished even when space in the symbiotic organ is available and ostensibly accessible for colonization. We speculate that resident symbionts exclude subsequent infections by manipulating the host environment, partially but not exclusively by eliciting tissue remodeling of the symbiont organ. IMPORTANCE Host-associated microbial communities underpin critical ecosystem processes and human health, and their ability to do so is determined in turn by the various processes that shape their composition. While selection deterministically acts on competing genotypes and species during community assembly, the manner by which selection determines the trajectory of community assembly can differ depending on the sequence by which taxa are established within that community. We document this phenomenon, known as a priority effect, during experimental colonization of a North American insect pest, the squash bug Anasa tristis, by its betaproteobacterial symbionts in the genus Caballeronia. Our study demonstrates how stark, strain-level variation can emerge in specialized host-microbe symbioses simply through differences in the order by which strains colonize the host. Understanding the mechanistic drivers of community structure in host-associated microbiomes can highlight both pitfalls and opportunities for the engineering of these communities and their constituent taxa for societal benefit.
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Affiliation(s)
- Jason Z Chen
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Anthony Junker
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Iris Zheng
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | | | - Nic M Vega
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Department of Physics, Emory University, Atlanta, Georgia, USA
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Fischer MT, Xue KS, Costello EK, Dvorak M, Raboisson G, Robaczewska A, Caty SN, Relman DA, O'Connell LA. Effects of parental care on skin microbial community composition in poison frogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612488. [PMID: 39314287 PMCID: PMC11419107 DOI: 10.1101/2024.09.11.612488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects. Early exposure to microbes can have lasting influences on the assembly and functionality of the host's microbiota, leaving a life-long imprint on host health and disease. Studies of the role played by parental care in microbial acquisition have primarily focused on humans and hosts with agricultural relevance. Anuran vertebrates offer the opportunity to examine microbial community composition across life stages as a function of parental investment. In this study, we investigate vertical transmission of microbiota during parental care in a poison frog (Family Dendrobatidae ), where fathers transport their offspring piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of the embryo begins after hatching from the vitelline envelope, emphasizing its potential role as microbial barrier during early development. Using a laboratory cross-foster experiment, we demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts the microbial skin communities of tadpoles in an ecologically relevant setting, we sampled frogs and tadpoles of sympatric species that do or do not exhibit tadpole transport in their natural habitat. We found more diverse microbial communities associated with tadpoles of transporting species compared to a non-transporting frog. However, we detected no difference in the degree of similarity between adult and tadpole skin microbiotas, based on whether the frog species exhibits transporting behavior or not. Using a field experiment, we confirmed that tadpole transport can result in the persistent colonization of tadpoles by isolated microbial taxa associated with the caregiver's skin, albeit often at low abundance. This is the first study to describe vertical transmission of skin microbes in anuran amphibians, showing that offspring transport may serve as a mechanism for transmission of parental skin microbes. Overall, these findings provide a foundation for further research on how vertical transmission in this order impacts host-associated microbiota and physiology.
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5
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Chen N, Hao L, Zhang Z, Qin C, Jie Z, Pan H, Duan J, Huang X, Zhang Y, Gao H, Lu R, Sun T, Yang H, Shi J, Liang M, Guo J, Gao Q, Zhao X, Dou Z, Xiao L, Zhang S, Jin X, Xu X, Yang H, Wang J, Jia H, Zhang T, Kristiansen K, Chen C, Zhu L. Insights into the assembly of the neovaginal microbiota in Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome patients. Nat Commun 2024; 15:7808. [PMID: 39242555 PMCID: PMC11379825 DOI: 10.1038/s41467-024-52102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/23/2024] [Indexed: 09/09/2024] Open
Abstract
Neovaginas are surgically constructed to correct uterovaginal agenesis in women with Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome or as part of gender-affirming surgery for transfeminine individuals. Understanding the assembly of the neovaginal microbiota is crucial for guiding its management. To address this, we conducted a longitudinal study on MRKH patients following laparoscopic peritoneal vaginoplasty. Our findings reveal that the early microbial assemblage exhibited stochastic characteristics, accompanied with a notable bloom of Enterococcus faecalis and genital Mycoplasmas. While both the pre-surgery dimple microbiota and the fecal microbiota constituted the primary species pool, the neovaginal microbiota developed into a microbiota that resembled that of a normal vagina at 6-12 months post-surgery, albeit with a bacterial vaginosis (BV)-like structure. By 2-4 years post-surgery, the neovaginal microbiota had further evolved into a structure closely resembling with the homeostatic pre-surgery dimple microbiota. This concords with the development of the squamous epithelium in the neovagina and highlights the pivotal roles of progressive selective forces imposed by the evolving neovaginal environment and the colonization tropism of vaginal species. Notably, we observed that strains of Lactobacillus crispatus colonizing the neovagina primarily originated from the dimple. Since L. crispatus is generally associated with vaginal health, this finding suggests potential avenues for future research to promote its colonization.
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Affiliation(s)
- Na Chen
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Lilan Hao
- BGI-Research, Shenzhen, 518083, China
- Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, 266555, China
| | - Zhe Zhang
- BGI-Research, Shenzhen, 518083, China
| | - Chenglu Qin
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, 518000, Guangdong, China
| | - Zhuye Jie
- BGI-Research, Shenzhen, 518083, China
- Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Hongxin Pan
- Department of Gynecology, Southern University of Science and Technology Hospital, 6019 liuxian street, Shenzhen, 518000, China
| | - Jiali Duan
- Chinese Academy of Medical Sciences & Peking Union Medical College, 4+4 Medical Doctor Program, No.9 Dongdansantiao, 100730, Beijing, China
| | - Xincheng Huang
- BGI-Research, Shenzhen, 518083, China
- China National GeneBank, BGI-Research, Shenzhen, 518210, China
| | - Yunhong Zhang
- Social Affairs Bureau of Suzhou National New and Hi-tech Industrial Development Zone, Suzhou, 215163, China
| | - Hongqin Gao
- Suzhou National New and Hi-tech Industrial Development Zone Center for Maternal and Child Health and Family Planning Service, Suzhou, 215163, China
| | - Ruike Lu
- Suzhou National New and Hi-tech Industrial Development Zone Center for Maternal and Child Health and Family Planning Service, Suzhou, 215163, China
| | - Tianshu Sun
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Hua Yang
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Jinqiu Shi
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, 518000, Guangdong, China
| | - Maolian Liang
- Department of Obstetrics and Gynaecology, The 3rd Affiliated Hospital of Shenzhen University, Luohu hospital, Shenzhen, 518000, Guangdong, China
| | - Jianbin Guo
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Qianqian Gao
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Xiaoyue Zhao
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Zhiyuan Dou
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China
| | - Liang Xiao
- BGI-Research, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, 266555, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Research, Shenzhen, 518083, China
| | | | - Xin Jin
- BGI-Research, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Research, Shenzhen, 518083, China
| | - Huanming Yang
- BGI-Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310013, China
| | - Jian Wang
- BGI-Research, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310013, China
| | - Huijue Jia
- BGI-Research, Shenzhen, 518083, China
- School of Life Sciences, Fudan University, Shanghai, 200433, China
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Tao Zhang
- BGI Research, Wuhan, 430074, China.
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, Shenzhen, Guangdong, 518083, China.
| | - Karsten Kristiansen
- BGI-Research, Shenzhen, 518083, China.
- Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Research, Qingdao, 266555, China.
| | - Chen Chen
- BGI-Research, Shenzhen, 518083, China.
- Department of Biology, Ole Maaløes Vej 5, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - Lan Zhu
- National Clinical Research Center for Obstetric and Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, State Key Laboratory for Complex Severe and Rare Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, 100005, Beijing, China.
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Shao Y, Garcia-Mauriño C, Clare S, Dawson NJR, Mu A, Adoum A, Harcourt K, Liu J, Browne HP, Stares MD, Rodger A, Brocklehurst P, Field N, Lawley TD. Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. Nat Microbiol 2024:10.1038/s41564-024-01804-9. [PMID: 39242817 DOI: 10.1038/s41564-024-01804-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/05/2024] [Indexed: 09/09/2024]
Abstract
Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.
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Affiliation(s)
- Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| | | | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas J R Dawson
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Anne Adoum
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Katherine Harcourt
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Junyan Liu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Alison Rodger
- Institute for Global Health, University College London, London, UK
| | - Peter Brocklehurst
- Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, UK
| | - Nigel Field
- Institute for Global Health, University College London, London, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
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7
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Hudcovic T, Petr Hermanova P, Kozakova H, Benada O, Kofronova O, Schwarzer M, Srutkova D. Priority order of neonatal colonization by a probiotic or pathogenic Escherichia coli strain dictates the host response to experimental colitis. Front Microbiol 2024; 15:1393732. [PMID: 39206364 PMCID: PMC11349737 DOI: 10.3389/fmicb.2024.1393732] [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: 02/29/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
The alarming prevalence of inflammatory bowel disease (IBD) in early childhood is associated with imbalances in the microbiome, the immune response, and environmental factors. Some pathogenic Escherichia coli (E. coli) strains have been found in IBD patients, where they may influence disease progression. Therefore, the discovery of new harmful bacterial strains that have the potential to drive the inflammatory response is of great importance. In this study, we compared the immunomodulatory properties of two E. coli strains of serotype O6: the probiotic E. coli Nissle 1917 and the uropathogenic E. coli O6:K13:H1. Using the epithelial Caco-2 cell line, we investigated the different abilities of the strains to adhere to and invade epithelial cells. We confirmed the potential of E. coli Nissle 1917 to modulate the Th1 immune response in a specific manner in an in vitro setting by stimulating mouse bone marrow-derived dendritic cells (BM-DCs). In gnotobiotic in vivo experiments, we demonstrated that neonatal colonization with E. coli Nissle 1917 achieves a stable high concentration in the intestine and protects mice from the progressive effect of E. coli O6:K13:H1 in developing ulcerative colitis in an experimental model. In contrast, a single-dose treatment with E. coli Nissle 1917 is ineffective in achieving such high concentrations and does not protect against DSS-induced ulcerative colitis in mice neonatally colonized with pathobiont E. coli O6:K13:H1. Despite the stable coexistence of both E. coli strains in the intestinal environment of the mice, we demonstrated a beneficial competitive interaction between the early colonizing E. coli Nissle 1917 and the late-arriving strain O6:K13:H1, suggesting its anti-inflammatory potential for the host. This study highlights the importance of the sequence of bacterial colonization, which influences the development of the immune response in the host gut and potentially impacts future quality of life.
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Affiliation(s)
- Tomas Hudcovic
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
| | - Petra Petr Hermanova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
| | - Hana Kozakova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
| | - Oldrich Benada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Olga Kofronova
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czechia
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8
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Bertero A, Banchi P, Del Carro A, Corrò M, Colitti B, Van Soom A, Bertolotti L, Rota A. Meconium microbiota in naturally delivered canine puppies. BMC Vet Res 2024; 20:363. [PMID: 39135043 PMCID: PMC11318152 DOI: 10.1186/s12917-024-04225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/06/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Microbial colonization during early life has a pivotal impact on the host health, shaping immune and metabolic functions, but little is known about timing and features of this process in dogs. The objectives of this study were to characterize the first step of intestinal microbiota development in naturally delivered canine puppies and to investigate its relationship with the maternal bacterial flora, using traditional culture and molecular analyses. Sixty puppies of two breeds, Appenzeller Cattle Dog (n = 3 dams) and Lagotto Romagnolo (n = 6), housed in the same breeding kennel, were included in the study. Swabs were collected in duplicate (for culture and for molecular analysis) from the dams' vagina and rectum at the end of parturition, from puppies' rectum, before maternal care, and from the environment (floor of the nursery and parturition box). RESULTS 93.3% meconium samples showed bacterial growth, limited to a few colonies in 57.0% of cases. High growth was detected for Enterococcus faecalis, which was the most frequently isolated bacterium. The genus Enterococcus was one of the most represented in the dams' rectum and vagina (88.9% and 55.6%, respectively). The genera Staphylococcus, Enterococcus, Escherichia and Proteus were also often isolated in meconium but were usually present in maternal samples as well, together with ubiquitous bacteria (Acinetobacter, Psychrobacter). In the environmental samples, just a few bacterial species were found, all with low microbial load. Additionally, bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were identified in meconium through molecular analysis, confirming the culture results and the early colonization of the newborn gut. Maternal, meconium and environmental samples had similar alpha diversity, while beta-diversity showed differences among families (i.e. a dam and her litter), and association indexes revealed a significant correlation between family members and between sample origin, suggesting a strong contribution of the maternal flora to the initial seeding of the canine neonatal gut and a strong individual dam imprint. CONCLUSION This study showed that the meconium of vaginally delivered puppies has its own microbiota immediately after birth, and that it is shaped by the dam, which gives a specific imprint to her litter.
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Affiliation(s)
- Alessia Bertero
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco (TO), Italy.
| | - Penelope Banchi
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco (TO), Italy
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Angela Del Carro
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco (TO), Italy
| | - Michela Corrò
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro (Padua), Italy
| | - Barbara Colitti
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco (TO), Italy
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Luigi Bertolotti
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco (TO), Italy
| | - Ada Rota
- Department of Veterinary Sciences, University of Turin, 10095, Grugliasco (TO), Italy
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9
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Ribère M, Lemieux-Labonté V, Pincez T, Azria E, Lapointe FJ. Duration of rupture of membranes and microbiome transmission to the newborn: A prospective study. BJOG 2024; 131:1249-1258. [PMID: 38311451 DOI: 10.1111/1471-0528.17774] [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: 09/21/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 02/06/2024]
Abstract
OBJECTIVE To assess whether labour variables (i.e. individuals characteristics, labour characteristics and medical interventions) impact maternal and newborn microbiomes. DESIGN Prospective monocentric study. SETTING Saint-Joseph Hospital tertiary maternity unit, in Paris, France. POPULATION All consecutive primiparous women with a physiological pregnancy and term labour from 15 April to 1 June 2017. METHODS 16S ribosomal RNA gene sequencing of the maternal vaginal, newborn skin and newborn oral microbiomes from 58 mother-baby dyads. MAIN OUTCOME MEASURES Analysis of the effects of 19 labour variables on the composition and diversity of these microbiomes. RESULTS The 19 labour variables explained a significant part of the variability in the vaginal, newborn oral and skin microbiomes (44%-67%). Strikingly, duration of rupture of membranes was the single factor that explained the greatest variability (adjusted R2: 7.7%-8.4%, p ≤ 0.002) and conditioned, by itself, the compositions of the three microbiomes under study. Long duration of rupture of membranes was specifically associated with a lower relative abundance of the Lactobacillus genus (1.7-fold to 68-fold reduction, p < 0.0001) as well as an increase in microbiome diversity, including genera implicated in nosocomial infections. The effects of duration of rupture of membranes were also present in newborns delivered by non-elective caesarean section. CONCLUSIONS Maternal and newborn microbiomes were greatly affected by labour variables. Duration of rupture of membranes, even in non-elective caesarean sections, should be considered in epidemiological and microbiological studies, as well as in vaginal seeding practices.
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Affiliation(s)
- Maïté Ribère
- Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | | | - Thomas Pincez
- Service d'Hématologie-Oncologie Pédiatrique, Centre de Cancérologie Charles-Bruneau, CHU Sainte-Justine, Département de Pédiatrie, Université de Montréal, Montréal, Québec, Canada
| | - Elie Azria
- Maternité Notre Dame de Bon Secours, Groupe Hospitalier Paris Saint-Joseph, Université Paris Cité, Paris, France
- UMR1153 - Obstetrical, Perinatal and Pediatric Epidemiology (EPOPé Research Team), FHU Prema, Université Paris Cité - INSERM, Paris, France
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10
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Vliex LMM, Penders J, Nauta A, Zoetendal EG, Blaak EE. The individual response to antibiotics and diet - insights into gut microbial resilience and host metabolism. Nat Rev Endocrinol 2024; 20:387-398. [PMID: 38486011 DOI: 10.1038/s41574-024-00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 06/16/2024]
Abstract
Antibiotic use disrupts microbial composition and activity in humans, but whether this disruption in turn affects host metabolic health is unclear. Cohort studies show associations between antibiotic use and an increased risk of developing obesity and type 2 diabetes mellitus. Here, we review available clinical trials and show the disruptive effect of antibiotic use on the gut microbiome in humans, as well as its impact on bile acid metabolism and microbial metabolites such as short-chain fatty acids. Placebo-controlled human studies do not show a consistent effect of antibiotic use on body weight and insulin sensitivity at a population level, but rather an individual-specific or subgroup-specific response. This response to antibiotic use is affected by the resistance and resilience of the gut microbiome, factors that determine the extent of disruption and the speed of recovery afterwards. Nutritional strategies to improve the composition and functionality of the gut microbiome, as well as its recovery after antibiotic use (for instance, with prebiotics), require a personalized approach to increase their efficacy. Improved insights into key factors that influence the individual-specific response to antibiotics and dietary intervention may lead to better efficacy in reversing or preventing antibiotic-induced microbial dysbiosis as well as strategies for preventing cardiometabolic diseases.
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Affiliation(s)
- Lars M M Vliex
- Department of Human Biology, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ellen E Blaak
- Department of Human Biology, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.
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11
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Henry LP, Fernandez M, Wolf S, Abhyankar V, Ayroles JF. Wolbachia impacts microbiome diversity and fitness-associated traits for Drosophila melanogaster in a seasonally fluctuating environment. Ecol Evol 2024; 14:e70004. [PMID: 39041013 PMCID: PMC11262851 DOI: 10.1002/ece3.70004] [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: 01/15/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/24/2024] Open
Abstract
The microbiome contributes to many different host traits, but its role in host adaptation remains enigmatic. The fitness benefits of the microbiome often depend on ecological conditions, but theory suggests that fluctuations in both the microbiome and environment modulate these fitness benefits. Moreover, vertically transmitted bacteria might constrain the ability of both the microbiome and host to respond to changing environments. Drosophila melanogaster provides an excellent system to investigate the impacts of interactions between the microbiome and the environment. To address this question, we created field mesocosms of D. melanogaster undergoing seasonal environmental change with and without the vertically transmitted bacteria, Wolbachia pipientis. Sampling temporal patterns in the microbiome revealed that Wolbachia constrained microbial diversity. Furthermore, Wolbachia and a dominant member of the microbiome, Commensalibacter, were associated with differences in two higher-order fitness traits, starvation resistance and lifespan. Our work here suggests that the interplay between the abiotic context and microbe-microbe interactions may shape key host phenotypes that underlie adaptation to changing environments. We conclude by exploring the consequences of complex interactions between Wolbachia and the microbiome for our understanding of eco-evolutionary processes that shape host-microbiome interactions.
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Affiliation(s)
- Lucas P. Henry
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
- Department of Biology, Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Michael Fernandez
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Scott Wolf
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Varada Abhyankar
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
| | - Julien F. Ayroles
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
- Lewis‐Sigler Institute for Integrative GenomicsPrinceton UniversityPrincetonNew JerseyUSA
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12
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Stroud JT, Delory BM, Barnes EM, Chase JM, De Meester L, Dieskau J, Grainger TN, Halliday FW, Kardol P, Knight TM, Ladouceur E, Little CJ, Roscher C, Sarneel JM, Temperton VM, van Steijn TLH, Werner CM, Wood CW, Fukami T. Priority effects transcend scales and disciplines in biology. Trends Ecol Evol 2024; 39:677-688. [PMID: 38508922 DOI: 10.1016/j.tree.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/22/2024]
Abstract
Although primarily studied through the lens of community ecology, phenomena consistent with priority effects appear to be widespread across many different scenarios spanning a broad range of spatial, temporal, and biological scales. However, communication between these research fields is inconsistent and has resulted in a fragmented co-citation landscape, likely due to the diversity of terms used to refer to priority effects across these fields. We review these related terms, and the biological contexts in which they are used, to facilitate greater cross-disciplinary cohesion in research on priority effects. In breaking down these semantic barriers, we aim to provide a framework to better understand the conditions and mechanisms of priority effects, and their consequences across spatial and temporal scales.
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Affiliation(s)
- J T Stroud
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | - B M Delory
- Institute of Ecology, Leuphana University Lüneburg, Lüneburg, Germany; Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, The Netherlands.
| | - E M Barnes
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - J M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - L De Meester
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB), Müggelseedamm 310, 12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, Königin-Luise-Strasse 1-3, 14195 Berlin, Germany; Laboratory of Aquatic Ecology, Evolution, and Conservation, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - J Dieskau
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Department of Geobotany and Botanical Garden, Martin-Luther University, Germany
| | - T N Grainger
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - F W Halliday
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - P Kardol
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - T M Knight
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Department of Community Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle (Saale), Germany; Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - E Ladouceur
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - C J Little
- School of Environmental Science, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - C Roscher
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; Department of Physiological Diversity, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - J M Sarneel
- Department of Ecology and Environmental Science, Umea University, 901 87 Umea, Sweden
| | - V M Temperton
- Institute of Ecology, Leuphana University Lüneburg, Lüneburg, Germany
| | - T L H van Steijn
- Department of Ecology and Environmental Science, Umea University, 901 87 Umea, Sweden
| | - C M Werner
- Department of Environmental Science, Policy, and Sustainability, Southern Oregon University, Ashland, OR 97520, USA
| | - C W Wood
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - T Fukami
- Departments of Biology and Earth System Science, Stanford University, Stanford, CA 94305, USA.
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13
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Stagaman K, Alexiev A, Sieler MJ, Hammer A, Kasschau KD, Truong L, Tanguay RL, Sharpton TJ. The zebrafish gut microbiome influences benzo[a]pyrene developmental neurobehavioral toxicity. Sci Rep 2024; 14:14618. [PMID: 38918492 PMCID: PMC11199668 DOI: 10.1038/s41598-024-65610-3] [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: 02/09/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
Early-life exposure to environmental toxicants like Benzo[a]pyrene (BaP) is associated with several health consequences in vertebrates (i.e., impaired or altered neurophysiological and behavioral development). Although toxicant impacts were initially studied relative to host physiology, recent studies suggest that the gut microbiome is a possible target and/or mediator of behavioral responses to chemical exposure in organisms, via the gut-brain axis. However, the connection between BaP exposure, gut microbiota, and developmental neurotoxicity remains understudied. Using a zebrafish model, we determined whether the gut microbiome influences BaP impacts on behavior development. Embryonic zebrafish were treated with increasing concentrations of BaP and allowed to grow to the larval life stage, during which they underwent behavioral testing and intestinal dissection for gut microbiome profiling via high-throughput sequencing. We found that exposure affected larval zebrafish microbiome diversity and composition in a manner tied to behavioral development: increasing concentrations of BaP were associated with increased taxonomic diversity, exposure was associated with unweighted UniFrac distance, and microbiome diversity and exposure predicted larval behavior. Further, a gnotobiotic zebrafish experiment clarified whether microbiome presence was associated with BaP exposure response and behavioral changes. We found that gut microbiome state altered the relationship between BaP exposure concentration and behavioral response. These results support the idea that the zebrafish gut microbiome is a determinant of the developmental neurotoxicity that results from chemical exposure.
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Affiliation(s)
- Keaton Stagaman
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Alexandra Alexiev
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Michael J Sieler
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Austin Hammer
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Lisa Truong
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Robyn L Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA.
- Department of Statistics, Oregon State University, Corvallis, OR, USA.
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14
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Xiao M, Zhang C, Duan H, Narbad A, Zhao J, Chen W, Zhai Q, Yu L, Tian F. Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health. NPJ Biofilms Microbiomes 2024; 10:47. [PMID: 38898089 PMCID: PMC11186840 DOI: 10.1038/s41522-024-00524-6] [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: 12/29/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Throughout the life span of a host, bifidobacteria have shown superior colonization and glycan abilities. Complex glycans, such as human milk oligosaccharides and plant glycans, that reach the colon are directly internalized by the transport system of bifidobacteria, cleaved into simple structures by extracellular glycosyl hydrolase, and transported to cells for fermentation. The glycan utilization of bifidobacteria introduces cross-feeding activities between bifidobacterial strains and other microbiota, which are influenced by host nutrition and regulate gut homeostasis. This review discusses bifidobacterial glycan utilization strategies, focusing on the cross-feeding involved in bifidobacteria and its potential health benefits. Furthermore, the impact of cross-feeding on the gut trophic niche of bifidobacteria and host health is also highlighted. This review provides novel insights into the interactions between microbe-microbe and host-microbe.
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Affiliation(s)
- Meifang Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Chuan Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Hui Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park Colney, Norwich, Norfolk, NR4 7UA, UK
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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15
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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [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: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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16
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Wang B, Ma F, Du X, Zhang G, Li J. Prediction of microbe-drug associations based on a modified graph attention variational autoencoder and random forest. Front Microbiol 2024; 15:1394302. [PMID: 38881658 PMCID: PMC11176502 DOI: 10.3389/fmicb.2024.1394302] [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: 03/01/2024] [Accepted: 05/10/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction The identification of microbe-drug associations can greatly facilitate drug research and development. Traditional methods for screening microbe-drug associations are time-consuming, manpower-intensive, and costly to conduct, so computational methods are a good alternative. However, most of them ignore the combination of abundant sequence, structural information, and microbe-drug network topology. Methods In this study, we developed a computational framework based on a modified graph attention variational autoencoder (MGAVAEMDA) to infer potential microbedrug associations by combining biological information with the variational autoencoder. In MGAVAEMDA, we first used multiple databases, which include microbial sequences, drug structures, and microbe-drug association databases, to establish two comprehensive feature matrices of microbes and drugs after multiple similarity computations, fusion, smoothing, and thresholding. Then, we employed a combination of variational autoencoder and graph attention to extract low-dimensional feature representations of microbes and drugs. Finally, the lowdimensional feature representation and graphical adjacency matrix were input into the random forest classifier to obtain the microbe-drug association score to identify the potential microbe-drug association. Moreover, in order to correct the model complexity and redundant calculation to improve efficiency, we introduced a modified graph convolutional neural network embedded into the variational autoencoder for computing low dimensional features. Results The experiment results demonstrate that the prediction performance of MGAVAEMDA is better than the five state-of-the-art methods. For the major measurements (AUC =0.9357, AUPR =0.9378), the relative improvements of MGAVAEMDA compared to the suboptimal methods are 1.76 and 1.47%, respectively. Discussion We conducted case studies on two drugs and found that more than 85% of the predicted associations have been reported in PubMed. The comprehensive experimental results validated the reliability of our models in accurately inferring potential microbe-drug associations.
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Affiliation(s)
- Bo Wang
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
- Heilongjiang Key Laboratory of Big Data Network Security Detection and Analysis, Qiqihar University, Qiqihar, China
| | - Fangjian Ma
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Xiaoxin Du
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Guangda Zhang
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Jingyou Li
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
- Heilongjiang Key Laboratory of Big Data Network Security Detection and Analysis, Qiqihar University, Qiqihar, China
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17
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Algavi YM, Borenstein E. Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics. Nat Commun 2024; 15:4447. [PMID: 38789466 PMCID: PMC11126695 DOI: 10.1038/s41467-024-48717-z] [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: 09/12/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Microorganisms frequently migrate from one ecosystem to another. Yet, despite the potential importance of this process in modulating the environment and the microbial ecosystem, our understanding of the fundamental forces that govern microbial dispersion is still lacking. Moreover, while theoretical models and in-vitro experiments have highlighted the contribution of species interactions to community assembly, identifying such interactions in vivo, specifically in communities as complex as the human gut, remains challenging. To address this gap, here we introduce a robust and rigorous computational framework, termed Relative Dispersion Ratio (RDR) analysis, and leverage data from well-characterized fecal microbiota transplant trials, to rigorously pinpoint dependencies between taxa during the colonization of human gastrointestinal tract. Our analysis identifies numerous pairwise dependencies between co-colonizing microbes during migration between gastrointestinal environments. We further demonstrate that identified dependencies agree with previously reported findings from in-vitro experiments and population-wide distribution patterns. Finally, we explore metabolic dependencies between these taxa and characterize the functional properties that facilitate effective dispersion. Collectively, our findings provide insights into the principles and determinants of community dynamics following ecological translocation, informing potential opportunities for precise community design.
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Affiliation(s)
- Yadid M Algavi
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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18
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Yao X, Nie W, Chen X, Zhang J, Wei J, Qiu Y, Liu K, Shao D, Liu H, Ma Z, Li Z, Li B. Two Enterococcus faecium Isolates Demonstrated Modulating Effects on the Dysbiosis of Mice Gut Microbiota Induced by Antibiotic Treatment. Int J Mol Sci 2024; 25:5405. [PMID: 38791443 PMCID: PMC11121104 DOI: 10.3390/ijms25105405] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Broad-spectrum antibiotics are frequently used to treat bacteria-induced infections, but the overuse of antibiotics may induce the gut microbiota dysbiosis and disrupt gastrointestinal tract function. Probiotics can be applied to restore disturbed gut microbiota and repair abnormal intestinal metabolism. In the present study, two strains of Enterococcus faecium (named DC-K7 and DC-K9) were isolated and characterized from the fecal samples of infant dogs. The genomic features of E. faecium DC-K7 and DC-K9 were analyzed, the carbohydrate-active enzyme (CAZyme)-encoding genes were predicted, and their abilities to produce short-chain fatty acids (SCFAs) were investigated. The bacteriocin-encoding genes in the genome sequences of E. faecium DC-K7 and DC-K9 were analyzed, and the gene cluster of Enterolysin-A, which encoded a 401-amino-acid peptide, was predicted. Moreover, the modulating effects of E. faecium DC-K7 and DC-K9 on the gut microbiota dysbiosis induced by antibiotics were analyzed. The current results demonstrated that oral administrations of E. faecium DC-K7 and DC-K9 could enhance the relative abundances of beneficial microbes and decrease the relative abundances of harmful microbes. Therefore, the isolated E. faecium DC-K7 and DC-K9 were proven to be able to alter the gut microbiota dysbiosis induced by antibiotic treatment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (X.Y.); (W.N.); (X.C.); (J.Z.); (J.W.); (Y.Q.); (K.L.); (D.S.); (H.L.); (Z.M.)
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (X.Y.); (W.N.); (X.C.); (J.Z.); (J.W.); (Y.Q.); (K.L.); (D.S.); (H.L.); (Z.M.)
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19
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Mancuso CP, Baker JS, Qu E, Tripp AD, Balogun IO, Lieberman TD. Intraspecies warfare restricts strain coexistence in human skin microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592803. [PMID: 38765968 PMCID: PMC11100718 DOI: 10.1101/2024.05.07.592803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Determining why only a fraction of encountered or applied bacterial strains engraft in a given person's microbiome is crucial for understanding and engineering these communities1. Previous work has established that metabolism can determine colonization success in vivo2-4, but relevance of bacterial warfare in preventing engraftment has been less explored. Here, we demonstrate that intraspecies warfare presents a significant barrier to strain transmission in the skin microbiome by profiling 14,884 pairwise interactions between Staphylococcus epidermidis cultured from eighteen human subjects from six families. We find that intraspecies antagonisms are abundant; these interactions are mechanistically diverse, independent of the relatedness between strains, and consistent with rapid evolution via horizontal gene transfer. Ability to antagonize more strains is associated with reaching a higher fraction of the on-person S. epidermidis community. Moreover, antagonisms are significantly depleted among strains residing on the same person relative to random assemblages. Two notable exceptions, in which bacteria evolved to become sensitive to antimicrobials found on the same host, are explained by mutations that provide phage resistance, contextualizing the importance of warfare among other lethal selective pressures. Taken together, our results emphasize that accounting for intraspecies bacterial warfare is essential to the design of long-lasting probiotic therapeutics.
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Affiliation(s)
- Christopher P. Mancuso
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Jacob S. Baker
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Evan Qu
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - A. Delphine Tripp
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Systems Biology, Harvard University; Cambridge, MA 02138, USA
| | - Ishaq O. Balogun
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02142, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02142, USA
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20
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Han S, An X, He X, Ren X, Sichone J, Wu X, Zhang Y, Wang H, Sun F. Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering. Microorganisms 2024; 12:858. [PMID: 38792687 PMCID: PMC11124218 DOI: 10.3390/microorganisms12050858] [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: 02/29/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.
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Affiliation(s)
- Shuaibo Han
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaojiao An
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xiaolong He
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xin Ren
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - John Sichone
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xinxing Wu
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Fangli Sun
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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21
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Chevée V, Hullahalli K, Dailey KG, Güereca L, Zhang C, Waldor MK, Portnoy DA. Temporal and spatial dynamics of Listeria monocytogenes central nervous system infection in mice. Proc Natl Acad Sci U S A 2024; 121:e2320311121. [PMID: 38635627 PMCID: PMC11046682 DOI: 10.1073/pnas.2320311121] [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: 11/18/2023] [Accepted: 02/22/2024] [Indexed: 04/20/2024] Open
Abstract
Listeria monocytogenes is a bacterial pathogen that can cause life-threatening central nervous system (CNS) infections. While mechanisms by which L. monocytogenes and other pathogens traffic to the brain have been studied, a quantitative understanding of the underlying dynamics of colonization and replication within the brain is still lacking. In this study, we used barcoded L. monocytogenes to quantify the bottlenecks and dissemination patterns that lead to cerebral infection. Following intravenous (IV) inoculation, multiple independent invasion events seeded all parts of the CNS from the blood, however, only one clone usually became dominant in the brain. Sequential IV inoculations and intracranial inoculations suggested that clones that had a temporal advantage (i.e., seeded the CNS first), rather than a spatial advantage (i.e., invaded a particular brain region), were the main drivers of clonal dominance. In a foodborne model of cerebral infection with immunocompromised mice, rare invasion events instead led to a highly infected yet monoclonal CNS. This restrictive bottleneck likely arose from pathogen transit into the blood, rather than directly from the blood to the brain. Collectively, our findings provide a detailed quantitative understanding of the L. monocytogenes population dynamics that lead to CNS infection and a framework for studying the dynamics of other cerebral infections.
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Affiliation(s)
- Victoria Chevée
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Karthik Hullahalli
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- HHMI, Bethesda, MD20815
| | - Katherine G. Dailey
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- HHMI, Bethesda, MD20815
| | - Leslie Güereca
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Chenyu Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Matthew K. Waldor
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA02115
- Department of Microbiology, Harvard Medical School, Boston, MA02115
- HHMI, Bethesda, MD20815
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720
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22
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Alsudayri A, Perelman S, Brewer M, Chura A, McDevitt M, Drerup C, Ye L. Gut microbiota regulate maturation and mitochondrial function of the nutrient-sensing enteroendocrine cell. Development 2024; 151:dev202544. [PMID: 38577841 PMCID: PMC11112165 DOI: 10.1242/dev.202544] [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: 11/14/2023] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Enteroendocrine cells (EECs) are crucial for sensing ingested nutrients and regulating feeding behavior. How gut microbiota regulate the nutrient-sensing EEC activity is unclear. Our transcriptomic analysis demonstrates that commensal microbiota colonization significantly increases the expression of many genes associated with mitochondrial function. Using new methods to image EEC cytoplasmic and mitochondrial Ca2+ activity in live zebrafish, our data revealed that it is dynamically regulated during the EEC development process. Mature EECs display an increased mitochondrial-to-cytoplasmic Ca2+ ratio. Mitochondria are evenly distributed in the cytoplasm of immature EECs. As EECs mature, their mitochondria are highly localized at the basal membrane where EEC vesicle secretion occurs. Conventionalized (CV) EECs, but not germ-free (GF) EECs, exhibit spontaneous low-amplitude Ca2+ fluctuation. The mitochondrial-to-cytoplasmic Ca2+ ratio is significantly higher in CV EECs. Nutrient stimulants, such as fatty acid, increase cytoplasmic Ca2+ in a subset of EECs and promote a sustained mitochondrial Ca2+ and ATP increase. However, the nutrient-induced EEC mitochondrial activation is nearly abolished in GF zebrafish. Together, our study reveals that commensal microbiota are crucial in supporting EEC mitochondrial function and maturation.
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Affiliation(s)
- Alfahdah Alsudayri
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Shane Perelman
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Melissa Brewer
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Annika Chura
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Madelyn McDevitt
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Catherine Drerup
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lihua Ye
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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23
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Ruuskanen S. Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes. J Exp Biol 2024; 227:jeb246024. [PMID: 38449325 DOI: 10.1242/jeb.246024] [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] [Indexed: 03/08/2024]
Abstract
Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.
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Affiliation(s)
- Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9C, 40500 Jyväskylä, Finland
- Department of Biology, University of Turku, Vesilinnankatu 5, 20500 Turku, Finland
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24
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Keum GB, Pandey S, Kim ES, Doo H, Kwak J, Ryu S, Choi Y, Kang J, Kim S, Kim HB. Understanding the Diversity and Roles of the Ruminal Microbiome. J Microbiol 2024; 62:217-230. [PMID: 38662310 DOI: 10.1007/s12275-024-00121-4] [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: 11/10/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.
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Affiliation(s)
- Gi Beom Keum
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sriniwas Pandey
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Eun Sol Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Hyunok Doo
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Jinok Kwak
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sumin Ryu
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Yejin Choi
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Juyoun Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Sheena Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
| | - Hyeun Bum Kim
- Department of Animal Biotechnology, Dankook University, Cheonan, 31116, Republic of Korea.
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25
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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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26
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Yang K, Liu W, Lin HM, Chen T, Yang T, Zhang B, Wen X. Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China. ENVIRONMENTAL RESEARCH 2024; 243:117749. [PMID: 38061589 DOI: 10.1016/j.envres.2023.117749] [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: 09/09/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023]
Abstract
The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.
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Affiliation(s)
- Kuo Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Wei Liu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui-Min Lin
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tan Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China
| | - Ting Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China
| | - Bing Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Research Center of Food Environment and Public Health Engineering, Minzu University of China, Beijing 100081, China.
| | - Xianghua Wen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, School of Environment, Tsinghua University, Beijing 100084, China.
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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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28
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Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB, Arrieta MC. Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition. MICROBIOME 2024; 12:22. [PMID: 38326891 PMCID: PMC10848358 DOI: 10.1186/s40168-023-01735-3] [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: 08/27/2023] [Accepted: 12/01/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND The gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age. These maturational patterns have been well-characterized for bacteria, but limited descriptions exist for other microbiota members, such as fungi. Further, our current understanding of the prevalence of different patterns of bacterial and fungal microbiome maturation and how inter-kingdom dynamics influence early-life microbiome establishment is limited. RESULTS We examined individual shifts in bacterial and fungal alpha diversity from 3 to 12 months of age in 100 infants from the CHILD Cohort Study. We identified divergent patterns of gut bacterial or fungal microbiome maturation in over 40% of infants, which were characterized by differences in community composition, inter-kingdom dynamics, and microbe-derived metabolites in urine, suggestive of alterations in the timing of ecosystem transitions. Known microbiome-modifying factors, such as formula feeding and delivery by C-section, were associated with atypical bacterial, but not fungal, microbiome maturation patterns. Instead, fungal microbiome maturation was influenced by prenatal exposure to artificially sweetened beverages and the bacterial microbiome, emphasizing the importance of inter-kingdom dynamics in early-life colonization patterns. CONCLUSIONS These findings highlight the ecological and environmental factors underlying atypical patterns of microbiome maturation in infants, and the need to incorporate multi-kingdom and individual-level perspectives in microbiome research to improve our understandings of gut microbiome maturation patterns in early life and how they relate to host health. Video Abstract.
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Affiliation(s)
- Emily M Mercer
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Center, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute (ACHRI), Calgary, AB, Canada
| | - Hena R Ramay
- International Microbiome Center, University of Calgary, Calgary, AB, Canada
| | - Shirin Moossavi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Louvain, Belgium
- VIB Center for Microbiology, VIB, Louvain, Belgium
| | | | - Myrtha E Reyna
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Allan B Becker
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Piush J Mandhane
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Theo J Moraes
- Department of Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Malcolm R Sears
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Padmaja Subbarao
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Translational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Meghan B Azad
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Manitoba Interdisciplinary Lactation Centre (MILC), Winnipeg, MB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada.
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada.
- International Microbiome Center, University of Calgary, Calgary, AB, Canada.
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute (ACHRI), Calgary, AB, Canada.
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29
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Decaestecker E, Van de Moortel B, Mukherjee S, Gurung A, Stoks R, De Meester L. Hierarchical eco-evo dynamics mediated by the gut microbiome. Trends Ecol Evol 2024; 39:165-174. [PMID: 37863775 DOI: 10.1016/j.tree.2023.09.013] [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: 04/17/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]
Abstract
The concept of eco-evolutionary (eco-evo) dynamics, stating that ecological and evolutionary processes occur at similar time scales and influence each other, has contributed to our understanding of responses of populations, communities, and ecosystems to environmental change. Phenotypes, central to these eco-evo processes, can be strongly impacted by the gut microbiome. The gut microbiome shapes eco-evo dynamics in the host community through its effects on the host phenotype. Complex eco-evo feedback loops between the gut microbiome and the host communities might thus be common. Bottom-up dynamics occur when eco-evo interactions shaping the gut microbiome affect host phenotypes with consequences at population, community, and ecosystem levels. Top-down dynamics occur when eco-evo dynamics shaping the host community structure the gut microbiome.
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Affiliation(s)
- Ellen Decaestecker
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium.
| | - Broos Van de Moortel
- Laboratory of Aquatic Biology, Interdisciplinary Research Facility Life Sciences, KU Leuven, KULAK, Campus Kortrijk, B-8500 Kortrijk, Belgium
| | - Shinjini Mukherjee
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Laboratory of Reproductive Genomics, KU Leuven, B-3000 Leuven, Belgium
| | - Aditi Gurung
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium
| | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, B-3000 Leuven, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, B-3000 Leuven, Belgium; Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), D-12587 Berlin, Germany; Institute of Biology, Freie Universität Berlin, D-14195 Berlin, Germany
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30
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Feng Z, Li N, Deng Y, Yu Y, Gao Q, Wang J, Chen S, Xing R. Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China. Ecol Evol 2024; 14:e11001. [PMID: 38352203 PMCID: PMC10862184 DOI: 10.1002/ece3.11001] [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: 05/07/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Soil microorganisms play vital roles in regulating multiple ecosystem functions. Recent studies have revealed that the rare microbial taxa (with extremely low relative abundances, which are still largely ignored) are also crucial in maintaining the health and biodiversity of the soil and may respond differently to environmental pressure. However, little is known about the soil community structures of abundant and rare taxa and their assembly processes in different soil layers on the Qinghai-Tibet Plateau (QTP). The present study investigated the community structure and assembly processes of soil abundant and rare microbial taxa on the northeastern edge of the QTP. Soil microbial abundance was defined by abundant taxa, whereas rare taxa contributed to soil microbial diversity. The results of null model show that the stochastic process ruled the assembly processes of all sub-communities. Dispersal limitation contributed more to the assembly of abundant microbial taxa in the different soil layers. In contrast, drift played a more critical role in the assembly processes of the rare microbial taxa. In addition, in contrast to previous studies, the abundant taxa played more important roles in co-occurrence networks, most likely because of the heterogeneity of the soil, the sparsity of amplicon sequencing, the sampling strategy, and the limited samples in the present study. The results of this study improve our understanding of soil microbiome assemblies on the QTP and highlight the role of abundant taxa in sustaining the stability of microbial co-occurrence networks in different soil layers.
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Affiliation(s)
- Zhilin Feng
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Na Li
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Yanfang Deng
- Service Center of Qilian Mountain National Park in Qinghai ProvinceXiningQinghaiChina
| | - Yao Yu
- Service Center of Qilian Mountain National Park in Qinghai ProvinceXiningQinghaiChina
| | - Qingbo Gao
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
| | - Jiuli Wang
- Qinghai Nationalities UniversityXiningQinghaiChina
| | - Shi‐long Chen
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
| | - Rui Xing
- Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
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31
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Koren O, Konnikova L, Brodin P, Mysorekar IU, Collado MC. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat Rev Gastroenterol Hepatol 2024; 21:35-45. [PMID: 38097774 DOI: 10.1038/s41575-023-00864-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiome has important roles in host metabolism and immunity, and microbial dysbiosis affects human physiology and health. Maternal immunity and microbial metabolites during pregnancy, microbial transfer during birth, and transfer of immune factors, microorganisms and metabolites via breastfeeding provide critical sources of early-life microbial and immune training, with important consequences for human health. Only a few studies have directly examined the interactions between the gut microbiome and the immune system during pregnancy, and the subsequent effect on offspring development. In this Review, we aim to describe how the maternal microbiome shapes overall pregnancy-associated maternal, fetal and early neonatal immune systems, focusing on the existing evidence and highlighting current gaps to promote further research.
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Affiliation(s)
- Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Liza Konnikova
- Department of Paediatrics and Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Petter Brodin
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Indira U Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain.
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32
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Namasivayam S, Tilves C, Ding H, Wu S, Domingue JC, Ruiz-Bedoya C, Shah A, Bohrnsen E, Schwarz B, Bacorn M, Chen Q, Levy S, Dominguez Bello MG, Jain SK, Sears CL, Mueller NT, Hourigan SK. Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice. Gut Microbes 2024; 16:2353394. [PMID: 38743047 PMCID: PMC11095576 DOI: 10.1080/19490976.2024.2353394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Exposing C-section infants to the maternal vaginal microbiome, coined "vaginal seeding", partially restores microbial colonization. However, whether vaginal seeding decreases metabolic disease risk is unknown. Therefore, we assessed the effect of vaginal seeding of human infants on adiposity in a murine model. Germ-free mice were colonized with transitional stool from human infants who received vaginal seeding or control (placebo) seeding in a double-blind randomized trial. There was a reduction in intraabdominal adipose tissue (IAAT) volume in male mice that received stool from vaginally seeded infants compared to control infants. Higher levels of isoleucine and lower levels of nucleic acid metabolites were observed in controls and correlated with increased IAAT. This suggests that early changes in the gut microbiome and metabolome caused by vaginal seeding have a positive impact on metabolic health.
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Affiliation(s)
- Sivaranjani Namasivayam
- Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Curtis Tilves
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, MD, USA
| | - Hua Ding
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shaoguang Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jada C Domingue
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Camilo Ruiz-Bedoya
- Center for Infection and Inflammation Imaging Research, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ankit Shah
- Inova Health System, Inova Women’s Hospital, Falls Church, VA, USA
| | - Eric Bohrnsen
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Hamilton, MT, USA
| | - Benjamin Schwarz
- Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Hamilton, MT, USA
| | - Mickayla Bacorn
- Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Qing Chen
- Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shira Levy
- Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maria Gloria Dominguez Bello
- Departments of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Humans and the microbiome program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Sanjay K Jain
- Center for Infection and Inflammation Imaging Research, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noel T Mueller
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, MD, USA
| | - Suchitra K Hourigan
- Clinical Microbiome Unit (CMU), Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Division of Pediatric Gastroenterology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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33
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Goldman DA, Xue KS, Parrott AB, Jeeda RR, Franzese LR, Lopez JG, Vila JCC, Petrov DA, Good BH, Relman DA, Huang KC. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569120. [PMID: 38076867 PMCID: PMC10705444 DOI: 10.1101/2023.11.29.569120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The long-term success of introduced populations depends on their initial size and ability to compete against existing residents, but it remains unclear how these factors collectively shape colonization. Here, we investigate how initial population (propagule) size and resource competition interact during community coalescence by systematically mixing eight pairs of in vitro microbial communities at ratios that vary over six orders of magnitude, and we compare our results to a neutral ecological model. Although the composition of the resulting co-cultures deviated substantially from neutral expectations, each co-culture contained species whose relative abundance depended on propagule size even after ~40 generations of growth. Using a consumer-resource model, we show that this dose-dependent colonization can arise when resident and introduced species have high niche overlap and consume shared resources at similar rates. This model predicts that propagule size will have larger, longer-lasting effects in diverse communities in which niche overlap is higher, and we experimentally confirm that strain isolates show stronger dose dependence when introduced into diverse communities than in pairwise co-culture. This work shows how neutral-like colonization dynamics can emerge from non-neutral resource competition and have lasting effects on the outcomes of community coalescence.
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Affiliation(s)
- Doran A. Goldman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katherine S. Xue
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Autumn B. Parrott
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Rashi R. Jeeda
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauryn R. Franzese
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jaime G. Lopez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jean C. C. Vila
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Benjamin H. Good
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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35
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Peng L, Hoban J, Joffe J, Smith AH, Carpenter M, Marcelis T, Patel V, Lynn-Bell N, Oliver KM, Russell JA. Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid. J Evol Biol 2023; 36:1712-1730. [PMID: 37702036 DOI: 10.1111/jeb.14216] [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: 02/01/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023]
Abstract
Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.
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Affiliation(s)
- Linyao Peng
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jessica Hoban
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jonah Joffe
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Andrew H Smith
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Melissa Carpenter
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Tracy Marcelis
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Vilas Patel
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Nicole Lynn-Bell
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Kerry M Oliver
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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Laursen MF, Roager HM. Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy. THE ISME JOURNAL 2023; 17:2452-2457. [PMID: 37816852 PMCID: PMC10689826 DOI: 10.1038/s41396-023-01525-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023]
Abstract
Despite the significant role of the gut microbiota in infant health and development, little is known about the ecological processes determining gut microbial community assembly. According to ecology theory, the timing and order of arrival of microbial species into an ecosystem affect microbial community assembly, a phenomenon termed priority effects. Bifidobacterium species are recognized as highly abundant early colonizers of the infant's gut, partly due to their ability to selectively utilize human milk oligosaccharides (HMOs) from breast milk. However, the role of priority effects in Bifidobacterium community assembly remains unclear. Here, we investigated the Bifidobacterium community assembly in the gut of 25 breastfed Danish infants longitudinally sampled throughout the first 6 months of life. Our results showed that the breastfed infants were often initially, but temporarily, dominated by suboptimal HMO-utilizing Bifidobacterium taxa, such as B. longum subsp. longum, before more efficient HMO-utilizers such as B. longum subsp. infantis, replaced the first colonizer as the dominant Bifidobacterium taxon. Subsequently, we validated this observation using gnotobiotic mice sequentially colonized with B. longum subsp. longum and B. longum subsp. infantis or vice versa, with or without supplementation of HMOs in the drinking water. The results showed that in the absence of HMOs, order of arrival determined dominance. Yet, when mice were supplemented with HMOs the strength of priority effects diminished, and B. longum subsp. infantis dominated regardless of colonization order. Our data demonstrate that the arrival order of Bifidobacterium taxa and the deterministic force of breast milk-derived HMOs, dictate Bifidobacterium community assembly in the infant's gut.
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Affiliation(s)
- Martin F Laursen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark.
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Nappi J, Goncalves P, Khan T, Majzoub ME, Grobler AS, Marzinelli EM, Thomas T, Egan S. Differential priority effects impact taxonomy and functionality of host-associated microbiomes. Mol Ecol 2023; 32:6278-6293. [PMID: 34995388 DOI: 10.1111/mec.16336] [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: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023]
Abstract
Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.
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Affiliation(s)
- Jadranka Nappi
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Priscila Goncalves
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Tahsin Khan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Marwan E Majzoub
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Anna Sophia Grobler
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Torsten Thomas
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
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Wu R, Shen R, Liang Z, Zheng S, Yang Y, Lu Q, Adrian L, Wang S. Improve Niche Colonization and Microbial Interactions for Organohalide-Respiring-Bacteria-Mediated Remediation of Chloroethene-Contaminated Sites. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17338-17352. [PMID: 37902991 DOI: 10.1021/acs.est.3c05932] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation is promising in in situ bioremediation of chloroethene-contaminated sites. The bioremediation efficiency of this approach is largely determined by the successful colonization of fastidious OHRB, which is highly dependent on the presence of proper growth niches and microbial interactions. In this study, based on two ecological principles (i.e., Priority Effects and Coexistence Theory), three strategies were developed to enhance niche colonization of OHRB, which were tested both in laboratory experiments and field applications: (i) preinoculation of a niche-preparing culture (NPC, being mainly constituted of fermenting bacteria and methanogens); (ii) staggered fermentation; and (iii) increased inoculation of CE40 (a Dehalococcoides-containing tetrachloroethene-to-ethene dechlorinating enrichment culture). Batch experimental results show significantly higher dechlorination efficiencies, as well as lower concentrations of volatile fatty acids (VFAs) and methane, in experimental sets with staggered fermentation and niche-preconditioning with NPC for 4 days (CE40_NPC-4) relative to control sets. Accordingly, a comparatively higher abundance of Dehalococcoides as major OHRB, together with a lower abundance of fermenting bacteria and methanogens, was observed in CE40_NPC-4 with staggered fermentation, which indicated the balanced syntrophic and competitive interactions between OHRB and other populations for the efficient dechlorination. Further experiments with microbial source tracking analyses suggested enhanced colonization of OHRB by increasing the inoculation ratio of CE40. The optimized conditions for enhanced colonization of OHRB were successfully employed for field bioremediation of trichloroethene (TCE, 0.3-1.4 mM)- and vinyl chloride (VC, ∼0.04 mM)-contaminated sites, resulting in 96.6% TCE and 99.7% VC dechlorination to ethene within 5 and 3 months, respectively. This study provides ecological principles-guided strategies for efficient bioremediation of chloroethene-contaminated sites, which may be also employed for removal of other emerging organohalide pollutants.
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Affiliation(s)
- Rifeng Wu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Rui Shen
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhiwei Liang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shengzhi Zheng
- China State Science Dingshi Environmental Engineering Co., Ltd., Beijing 100102, China
| | - Yong Yang
- China State Science Dingshi Environmental Engineering Co., Ltd., Beijing 100102, China
| | - Qihong Lu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Lorenz Adrian
- Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Shanquan Wang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
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Subramanian P, Romero-Soto HN, Stern DB, Maxwell GL, Levy S, Hourigan SK. Delivery mode impacts gut bacteriophage colonization during infancy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.13.23298307. [PMID: 38014162 PMCID: PMC10680904 DOI: 10.1101/2023.11.13.23298307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages can alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. To begin to address this we examined how delivery mode affected bacteriophage colonization over the first two years of life. Results Shotgun metagenomic sequencing was conducted on 272 serial stool samples from 55 infants, collected at 1-2 days of life and 2, 6, 12 and 24 months. 33/55 (60%) infants were born by vaginal delivery. DNA viruses were identified, and by host inference, 94% of the viral sequences were found to be bacteriophages. Alpha diversity of the virome was increased in vaginally delivered infants compared to cesarean section delivered infants at 2 months (Shannon index, p=0.022). Beta diversity significantly differed by delivery mode at 2, 6, and 12 months when stratified by peripartum antibiotic use (Bray-Curtis dissimilarity, all p<0.05). Significant differentially abundant predicted bacteriophage hosts by delivery mode were seen at all time points. Moreover, there were differences in predicted bacteriophage functional gene abundances up to 24 months by delivery mode. Many of the functions considered to play a role in host response were increased in vaginal delivery. Conclusions Clear differences in bacteriophage composition and function were seen by delivery mode over the first two years of life. Given that phages are known to affect host immune response, our results suggest that future investigation into how delivery mode may lead to adverse inflammatory outcomes should not only include bacterial microbial colonization but also the potential role of bacteriophages and transkingdom interactions.
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Affiliation(s)
- Poorani Subramanian
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Hector N Romero-Soto
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - David B Stern
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - George L Maxwell
- Women's Service Line, Inova Health System, Falls Church, Virginia, United States
| | - Shira Levy
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
| | - Suchitra K Hourigan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States
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Alsudayri A, Perelman S, Chura A, Brewer M, McDevitt M, Drerup C, Ye L. Gut microbiota promotes enteroendocrine cell maturation and mitochondrial function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.558332. [PMID: 37961164 PMCID: PMC10635018 DOI: 10.1101/2023.09.27.558332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The enteroendocrine cells (EECs) in the intestine are crucial for sensing ingested nutrients and regulating feeding behavior. The means by which gut microbiota regulates the nutrient-sensing EEC activity is unclear. Our transcriptomic analysis of the EECs from germ-free (GF) and conventionalized (CV) zebrafish revealed that commensal microbiota colonization significantly increased the expression of many genes that are associated with mitochondrial function. Using in vivo imaging and 3D automated cell tracking approach, we developed new methods to image and analyze the EECs' cytoplasmic and mitochondrial calcium activity at cellular resolution in live zebrafish. Our data revealed that during the development, shortly after gut microbiota colonization, EECs briefly increased cytoplasm and mitochondrial Ca2+, a phenomenon we referred to as "EEC awakening". Following the EEC awakening, cytoplasmic Ca2+ levels but not mitochondrial Ca2+ level in the EECs decreased, resulting in a consistent increase in the mitochondrial-to-cytoplasmic Ca2+ ratio. The increased mitochondrial-to-cytoplasmic Ca2+ ratio is associated with the EEC maturation process. In immature EECs, we further discovered that their mitochondria are evenly distributed in the cytoplasm. When EECs mature, their mitochondria are highly localized in the basal lateral membrane where EEC vesicle secretion occurs. Furthermore, CV EECs, but not GF EECs, exhibit spontaneous low-amplitude calcium fluctuation. The mitochondrial-to-cytoplasm Ca2+ ratio is significantly higher in CV EECs. When stimulating the CV zebrafish with nutrients like fatty acids, nutrient stimulants increase cytoplasmic Ca2+ in a subset of EECs and promote a sustained mitochondrial Ca2+ increase. However, the nutrient induced EEC mitochondrial activation is nearly abolished in GF zebrafish. Together, our study reveals that commensal microbiota are critical in supporting EEC mitochondrial function and maturation. Selectively manipulating gut microbial signals to alter EEC mitochondrial function will provide new opportunities to change gut-brain nutrient sensing efficiency and feeding behavior.
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Affiliation(s)
- Alfahdah Alsudayri
- Department of Neuroscience, the Ohio State University Wexner Medical Center
| | - Shane Perelman
- Department of Neuroscience, the Ohio State University Wexner Medical Center
| | - Annika Chura
- Department of Neuroscience, the Ohio State University Wexner Medical Center
| | - Melissa Brewer
- Department of Neuroscience, the Ohio State University Wexner Medical Center
| | - Madelyn McDevitt
- Department of Neuroscience, the Ohio State University Wexner Medical Center
| | - Catherine Drerup
- Department of Integrative Biology, University of Wisconsin-Madison
| | - Lihua Ye
- Department of Neuroscience, the Ohio State University Wexner Medical Center
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Lumpi T, Guo X, Lindström ES. Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence. Environ Microbiol 2023; 25:2289-2302. [PMID: 37381117 DOI: 10.1111/1462-2920.16450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.
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Affiliation(s)
- Theresa Lumpi
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Xin Guo
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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Yu X, Ma F, Dai H, Liu J, Hashem NM, Sun P. Effects of Different Galacto-Oligosaccharide Supplementation on Growth Performance, Immune Function, Serum Nutrients, and Appetite-Related Hormones in Holstein Calves. Animals (Basel) 2023; 13:3366. [PMID: 37958121 PMCID: PMC10649109 DOI: 10.3390/ani13213366] [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: 09/07/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Our previous study showed that early supplementation with 10 g/(d·head) of galacto-oligosaccharides (GOS) in newborn Holstein dairy calves reduced the incidence of diarrhea and improved growth performance and mineral absorption. Since the dose of 10 g/(d·head) was the lowest by dose screening in our previous study, the present study was designed to investigate whether a lower amount of GOS has similar effects on growth performance, immune function, serum nutrients in newborn Holstein heifer calves, and to further investigate its effect on appetite-related hormones. Twenty-eight healthy newborn (1 day of age) Holstein heifers with similar average body weight (41.18 ± 1.90 kg) were randomly divided into four groups (n = 7): the control group (CON group), which received heated raw milk, and three experimental groups, which received heated raw milk supplemented with 2.5 (GOS2.5 group), 5 (GOS5 group), and 10 g/(d·head) (GOS10 group) GOS. All heifer calves were fed the same starter for 28 d. Supplementation with GOS linearly increased the final body weight, average daily gain, and feed efficiency in heifer calves (p < 0.01). Compared with the control group, the average daily gain and feed efficiency of heifer calves were significantly higher in the GOS5 and GOS10 groups than in the control group (p < 0.05). Furthermore, supplementation with GOS quadratically enhanced the starter and total average daily feed intake of the heifers (p < 0.01), especially in the GOS2.5 and GOS5 groups, (p < 0.05 vs. CON). The serum concentration of immunoglobulin A was linearly increased by GOS supplementation (p < 0.05), and the levels in the GOS5 and GOS10 groups were significantly higher than those in the CON group. Meanwhile, GOS linearly decreased serum interleukin-1β and interleukin-6 concentrations (p < 0.05). The serum concentration of triglycerides was also linearly decreased (p < 0.05), whereas total protein and blood urea nitrogen were linearly increased (p < 0.05). Supplementation with GOS linearly decreased the serum concentration of leptin (p < 0.05) but increased cholecystokinin and glucagon-like peptide-1 (p < 0.05). Increasing doses of GOS linearly improved serum calcium and copper concentrations (p < 0.01) and quadratically enhanced the concentration of magnesium, which peaked in the GOS5 group (p < 0.05). In conclusion, GOS supplementation reduced the incidence of diarrhea and improved the growth performance and immune function of Holstein heifer calves.
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Affiliation(s)
- Xin Yu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengtao Ma
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haonan Dai
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junhao Liu
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nesrein M. Hashem
- Department of Animal and Fish Production, Faculty of Agriculture, Alexandria University, Alexandria 21545, Egypt;
| | - Peng Sun
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Tremblay A, Bronner S, Binda S. Review and Perspectives on Bifidobacterium lactis for Infants' and Children's Health. Microorganisms 2023; 11:2501. [PMID: 37894159 PMCID: PMC10609373 DOI: 10.3390/microorganisms11102501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The influence of microbiota dysbiosis in early life is increasingly recognized as a risk factor for the development of several chronic diseases later in life, including an increased risk of asthma, eczema, allergies, obesity, and neurodevelopmental disorders. The question whether the potential lifelong consequences of early life dysbiosis could be mitigated by restoring microbiota composition remains unresolved. However, the current evidence base suggests that protecting the normal development of the microbiome during this critical developmental window could represent a valuable public health strategy to curb the incidence of chronic and lifestyle-related diseases. Probiotic Bifidobacteria are likely candidates for this purpose in newborns and infants considering the natural dominance of this genus on microbiota composition in early life. Moreover, the most frequently reported microbiota composition alteration in association with newborn and infant diseases, including necrotizing enterocolitis and diarrhea, is a reduction in Bifidobacteria levels. Several studies have assessed the effects of B. animalis subsp. lactis strains in newborns and infants, but recent expert opinions recommend analyzing their efficacy at the strain-specific level. Hence, using the B94 strain as an example, this review summarizes the clinical evidence available in infants and children in various indications, discussing the safety and potential modes of actions while providing perspectives on the concept of "non-infant-type" probiotics for infants' health.
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Affiliation(s)
- Annie Tremblay
- Rosell Institute for Microbiome and Probiotics, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada; (A.T.); (S.B.)
| | - Stéphane Bronner
- Rosell Institute for Microbiome and Probiotics, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada; (A.T.); (S.B.)
| | - Sylvie Binda
- Rosell Institute for Microbiome and Probiotics, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada; (A.T.); (S.B.)
- Lallemand Health Solutions, 19 Rue des Briquetiers, BP 59, 31702 Toulouse, France
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Xue S, Abdullahi R, Wu N, Zheng J, Su M, Xu M. Gut microecological regulation on bronchiolitis and asthma in children: A review. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:975-985. [PMID: 37105551 PMCID: PMC10542989 DOI: 10.1111/crj.13622] [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: 07/21/2022] [Revised: 02/22/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023]
Abstract
INTRODUCTION Asthma and bronchiolitis in children are considered common clinical problems associated with gut microbiota. However, the exact relationship between gut microbiota and the above-mentioned diseases remains unclear. Here, we discussed recent advances in understanding the potential mechanism underlying immune regulation of gut microbiota on asthma and bronchiolitis in children as well as the role of the gut-lung axis. METHODS We retrieved and assessed all relevant original articles related to gut microbiota, airway inflammation-induced wheezing in children, and gut-lung axis studies from databases that have been published so far, including PubMed/MEDLINE, Scopus, Google Scholar, China National Knowledge Infrastructure (CNKI) and the Wanfang Database. RESULTS The infant period is critical for the development of gut microbiota, which can be influenced by gestational age, delivery mode, antibiotic exposure and feeding mode. The gut microbiota in children with asthma and bronchiolitis is significantly distinct from those in healthy subjects. Gut microbiota dysbiosis is implicated in asthma and bronchiolitis in children. The presence of intestinal disturbances in lung diseases highlights the importance of the gut-lung axis. CONCLUSION Gut microbiota dysbiosis potentially increases the risk of asthma and bronchiolitis in children. Moreover, a deeper understanding of the gut-lung axis with regard to the gut microbiota of children with respiratory diseases could contribute to clinical practice for pulmonary diseases.
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Affiliation(s)
- Sichen Xue
- Department of PediatricsThe First Affiliated Hospital of Ningbo UniversityNingboZhejiangChina
- Department of Pediatric Respiratory MedicineThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Rukkaiya Abdullahi
- Department of Pediatric Respiratory MedicineThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Naisheng Wu
- Department of PediatricsThe First Affiliated Hospital of Ningbo UniversityNingboZhejiangChina
| | - Jishan Zheng
- Department of PediatricsThe Ningbo Women and Children's HospitalNingboChina
| | - Miaoshang Su
- Department of Pediatric Respiratory MedicineThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouZhejiangChina
| | - Manhuan Xu
- College of Laboratory Medicine and Life ScienceWenzhou Medical UniversityWenzhouZhejiangChina
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Liu YC, Chen TH, Huang YF, Chen CL, Nai YS. Investigation of the fall armyworm (Spodoptera frugiperda) gut microbiome and entomopathogenic fungus-induced pathobiome. J Invertebr Pathol 2023; 200:107976. [PMID: 37541570 DOI: 10.1016/j.jip.2023.107976] [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: 03/24/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 08/06/2023]
Abstract
The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both cornfield and laboratory-reared populations was investigated using a 16S metagenomic approach. The alpha- and beta-diversity of the cornfield FAW populations varied among sampling sites and were higher than those of the laboratory-reared FAW population, indicating that different diets and environments influence the gut bacterial composition. To better understand the interaction between the microbiome and entomopathogenic fungi (EPF), FAWs from organic and conventionally managed corn fields and from the laboratory-reared colony were inoculated with Beauveria bassiana NCHU-153 (Bb-NCHU-153). A longer median lethal time (LT50) was observed in the Bb-NCHU-153-infected cornfield FAW population than in the laboratory-reared FAWs. In terms of the microbiome, three Bb-NCHU-153-infected FAW groups showed different gut bacterial compositions compared to noninfected FAW. Further investigation of the cooccurrence network and linear discriminant analysis (LDA) of effect size (LEfSe) revealed that the enriched bacterial genera, such as Enterococcus, Serratia, Achromobacter, and Tsukamurella, in the gut might play the role of opportunistic pathogens after fungal infection; in contrast, some gut bacteria of Methylobacterium, Marinomonas, Paenochrobactrum, Pseudomonas, Acinetobacter, Delftia, Dietzia, Gordonia, Leucobacter, Paracoccus, and Stenotrophomonas might be probiotics against EPF infection. These results indicated that EPF infection can change the gut bacterial composition and lead to a pathobiome in the FAW and that some bacterial species might protect the FAW from EPF infection. These findings could be applied to the design of pathobiome-inducing biocontrol strategies.
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Affiliation(s)
- Yao-Chia Liu
- Department of Entomology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Tzu-Han Chen
- Department of Entomology, National Chung-Hsing University, Taichung 402, Taiwan
| | - Yu-Feng Huang
- Department of Entomology, National Chung-Hsing University, Taichung 402, Taiwan; Department of Computer Science and Engineering, Yuan-Ze University, Tao-Yuan City 32003, Taiwan
| | - Chang-Lin Chen
- Department of Horticulture, National Chung-Hsing University, Taichung 402, Taiwan
| | - Yu-Shin Nai
- Department of Entomology, National Chung-Hsing University, Taichung 402, Taiwan.
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Brown KL, Ganswindt A, Steenkamp G, Tordiffe ASW. Responses to Reduced Feeding Frequency in Captive-Born Cheetahs ( Acinonyx jubatus): Implications for Behavioural and Physiological Stress and Gastrointestinal Health. Animals (Basel) 2023; 13:2783. [PMID: 37685047 PMCID: PMC10486355 DOI: 10.3390/ani13172783] [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: 08/02/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Unnatural diet composition and frequent feeding regimes may play an aetiological role in the multiple diseases prevalent in captive cheetahs. This study investigated the responses of captive-born (hand-reared) cheetahs (n = 6) to a reduced feeding frequency schedule distinguished by offering larger quantities of food less frequently. The study cheetahs were fed four once-daily meals per week during the 3-week treatment period, followed by a 3-week control period in which they were fed two daily rations six days a week. Total weekly food intake was maintained throughout the study. Variations in behaviour, faecal consistency score (FCS), and faecal glucocorticoid metabolite concentration were measured. Less frequent feeding resulted in higher FCS (p < 0.01) and locomotory behaviour (p < 0.05) among the studied cheetahs. Faecal glucocorticoid metabolite concentration demonstrated an initial acute stress response to the change in feeding frequency (p < 0.05) and subsequent adaptation. The results of the FCS analysis suggest that the more natural feeding pattern could have benefited the studied cheetahs' gastrointestinal health without a significant behavioural or physiological stress response overall to the change in feeding frequency.
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Affiliation(s)
- Kelsey Lee Brown
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
- Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
| | - André Ganswindt
- Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, Mammal Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Gerhard Steenkamp
- Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
| | - Adrian Stephen Wolferstan Tordiffe
- Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
- Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
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47
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Guex I, Mazza C, Dubey M, Batsch M, Li R, van der Meer JR. Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding. PLoS Comput Biol 2023; 19:e1011402. [PMID: 37603551 PMCID: PMC10470959 DOI: 10.1371/journal.pcbi.1011402] [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: 02/13/2023] [Revised: 08/31/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
When bacterial species with the same resource preferences share the same growth environment, it is commonly believed that direct competition will arise. A large variety of competition and more general 'interaction' models have been formulated, but what is currently lacking are models that link monoculture growth kinetics and community growth under inclusion of emerging biological interactions, such as metabolite cross-feeding. In order to understand and mathematically describe the nature of potential cross-feeding interactions, we design experiments where two bacterial species Pseudomonas putida and Pseudomonas veronii grow in liquid medium either in mono- or as co-culture in a resource-limited environment. We measure population growth under single substrate competition or with double species-specific substrates (substrate 'indifference'), and starting from varying cell ratios of either species. Using experimental data as input, we first consider a mean-field model of resource-based competition, which captures well the empirically observed growth rates for monocultures, but fails to correctly predict growth rates in co-culture mixtures, in particular for skewed starting species ratios. Based on this, we extend the model by cross-feeding interactions where the consumption of substrate by one consumer produces metabolites that in turn are resources for the other consumer, thus leading to positive feedback in the species system. Two different cross-feeding options were considered, which either lead to constant metabolite cross-feeding, or to a regulated form, where metabolite utilization is activated with rates according to either a threshold or a Hill function, dependent on metabolite concentration. Both mathematical proof and experimental data indicate regulated cross-feeding to be the preferred model to constant metabolite utilization, with best co-culture growth predictions in case of high Hill coefficients, close to binary (on/off) activation states. This suggests that species use the appearing metabolite concentrations only when they are becoming high enough; possibly as a consequence of their lower energetic content than the primary substrate. Metabolite sharing was particularly relevant at unbalanced starting cell ratios, causing the minority partner to proliferate more than expected from the competitive substrate because of metabolite release from the majority partner. This effect thus likely quells immediate substrate competition and may be important in natural communities with typical very skewed relative taxa abundances and slower-growing taxa. In conclusion, the regulated bacterial interaction network correctly describes species substrate growth reactions in mixtures with few kinetic parameters that can be obtained from monoculture growth experiments.
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Affiliation(s)
- Isaline Guex
- Department of Mathematics, University of Fribourg, Fribourg, Switzerland
| | - Christian Mazza
- Department of Mathematics, University of Fribourg, Fribourg, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Maxime Batsch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Renyi Li
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Miller AJ, Gass J, Jo MC, Bishop L, Petereit J, Woodhams DC, Voyles J. Towards the generation of gnotobiotic larvae as a tool to investigate the influence of the microbiome on the development of the amphibian immune system. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220125. [PMID: 37305911 PMCID: PMC10258664 DOI: 10.1098/rstb.2022.0125] [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: 09/01/2022] [Accepted: 11/28/2022] [Indexed: 06/13/2023] Open
Abstract
The immune equilibrium model suggests that exposure to microbes during early life primes immune responses for pathogen exposure later in life. While recent studies using a range of gnotobiotic (germ-free) model organisms offer support for this theory, we currently lack a tractable model system for investigating the influence of the microbiome on immune system development. Here, we used an amphibian species (Xenopus laevis) to investigate the importance of the microbiome in larval development and susceptibility to infectious disease later in life. We found that experimental reductions of the microbiome during embryonic and larval stages effectively reduced microbial richness, diversity and altered community composition in tadpoles prior to metamorphosis. In addition, our antimicrobial treatments resulted in few negative effects on larval development, body condition, or survival to metamorphosis. However, contrary to our predictions, our antimicrobial treatments did not alter susceptibility to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in the adult life stage. While our treatments to reduce the microbiome during early development did not play a critical role in determining susceptibility to disease caused by Bd in X. laevis, they nevertheless indicate that developing a gnotobiotic amphibian model system may be highly useful for future immunological investigations. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.
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Affiliation(s)
| | - Jordan Gass
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Myung Chul Jo
- Environmental Health and Safety, University of Nevada, Reno, NV 89557, USA
| | - Lucas Bishop
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
| | | | - Jamie Voyles
- Department of Biology, University of Nevada, Reno, NV 89557, USA
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Zhou L, Qiu W, Wang J, Zhao A, Zhou C, Sun T, Xiong Z, Cao P, Shen W, Chen J, Lai X, Zhao LH, Wu Y, Li M, Qiu F, Yu Y, Xu ZZ, Zhou H, Jia W, Liao Y, Retnakaran R, Krewski D, Wen SW, Clemente JC, Chen T, Xie RH, He Y. Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial. Cell Host Microbe 2023; 31:1232-1247.e5. [PMID: 37327780 DOI: 10.1016/j.chom.2023.05.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/22/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
The microbiomes of cesarean-born infants differ from vaginally delivered infants and are associated with increased disease risks. Vaginal microbiota transfer (VMT) to newborns may reverse C-section-related microbiome disturbances. Here, we evaluated the effect of VMT by exposing newborns to maternal vaginal fluids and assessing neurodevelopment, as well as the fecal microbiota and metabolome. Sixty-eight cesarean-delivered infants were randomly assigned a VMT or saline gauze intervention immediately after delivery in a triple-blind manner (ChiCTR2000031326). Adverse events were not significantly different between the two groups. Infant neurodevelopment, as measured by the Ages and Stages Questionnaire (ASQ-3) score at 6 months, was significantly higher with VMT than saline. VMT significantly accelerated gut microbiota maturation and regulated levels of certain fecal metabolites and metabolic functions, including carbohydrate, energy, and amino acid metabolisms, within 42 days after birth. Overall, VMT is likely safe and may partially normalize neurodevelopment and the fecal microbiome in cesarean-delivered infants.
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Affiliation(s)
- Lepeng Zhou
- School of Nursing, Affiliated Foshan Maternity & Child Healthcare Hospital, Department of Laboratory Medicine in Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China; Department of Nursing, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Wen Qiu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
| | - Jie Wang
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Aihua Zhao
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Chuhui Zhou
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Tao Sun
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Ziyu Xiong
- Department of Nursing, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Peihua Cao
- Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Shen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jingfen Chen
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Xiaolu Lai
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Liu-Hong Zhao
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China
| | - Yue Wu
- Department of Cardiology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Meng Li
- Department of Obstetrics, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Feng Qiu
- Department of Laboratory Medicine, The Seventh Affiliated Hospital, Southern Medical University, Foshan, Guangdong 528244, China
| | - Yanhong Yu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zhenjiang Zech Xu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Food Science and Technology, Institute of Nutrition and College of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Wei Jia
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yan Liao
- Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada
| | - Ravi Retnakaran
- Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Division of Endocrinology, University of Toronto, Toronto, ON M5S 2E8, Canada
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, Faculty of Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Risk Science International, Ottawa, ON K1P 5J6, Canada; School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Shi Wu Wen
- Ottawa Hospital Research Institute, Ottawa, ON K1H8L6, Canada; School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jose C Clemente
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Tianlu Chen
- Center for Translational Medicine and Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai 200233, China.
| | - Ri-Hua Xie
- School of Nursing; Department of Nursing, Foshan Fetal Medicine Research Institute, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong 528100, China.
| | - Yan He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China; State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, Guangdong 510515, China; Guangdong Provincial Clinical Research Center for Laboratory Medicine, Guangzhou, Guangdong 510033, China.
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50
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Pan Q, Huang J, Zhang S, Qin H, Dong Y, Wang X, Mu Y, Tang H, Zhou R. Synergistic effect of biotic and abiotic factors drives microbiota succession and assembly in medium-temperature Daqu. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4392-4400. [PMID: 36891660 DOI: 10.1002/jsfa.12543] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/08/2023] [Accepted: 03/09/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND The feasibility of fortification techniques to improve the quality of medium-temperature Daqu (MTD) by inoculation functional isolates has been demonstrated. However, it is unclear what is the effect of inoculation on the controllability during the MTD fermentation process. Here, inoculated a single strain of Bacillus licheniformis, and the microbiota composed of Bacillus velezensis and Bacillus subtilis, were used to investigate the synergistic effect of biotic and abiotic factors on the succession and assembly of the MTD microbiota during the process. RESULTS The biotic factors promoted the proliferation of microorganisms that arrived early at the MTD. Subsequently, this alteration might inhibit microorganisms that colonized later in the MTD microecosystem, thereby assembling a different but more stable microbial community. Moreover, the biotic factors making bacterial community assembly were dominated by variable selection earlier, whereas the fungal community assembly was dominated mainly by extreme abiotic factors rather than biotic factors. Interestingly, fermentation temperature and moisture were significantly associated with the succession and assembly of the fortified MTD community. Meanwhile, the effect of the environmental variables on endogenous variables was also significant. Thus, changes in endogenous variables could be mitigated by adjusting environmental variables to regulate the process of MTD fermentation. CONCLUSION Biotic factors cause rapid changes of the microbiota during the MTD fermentation process, which could be controlled indirectly by regulating environmental variables. Meanwhile, a more stable MTD ecological network might be beneficial for enhancing the stability of MTD quality. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Qianglin Pan
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | | | - Hui Qin
- Luzhou Lao Jiao Co., Ltd, Luzhou, China
| | - Yi Dong
- Luzhou Lao Jiao Co., Ltd, Luzhou, China
| | | | - Yu Mu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Huifang Tang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
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