1
|
Le VV, Ko SR, Shin Y, Kim K, Ahn CY. Succession of particle-attached and free-living bacterial communities in response to microalgal dynamics induced by the biological cyanocide paucibactin A. CHEMOSPHERE 2024; 358:142197. [PMID: 38692365 DOI: 10.1016/j.chemosphere.2024.142197] [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: 02/02/2024] [Revised: 04/05/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Microalgae, including cyanobacteria and eukaryotic algae, are hotspots of primary production and play a critical role in global carbon cycling. However, these species often form blooms that poses a threat to aquatic ecosystems. Although the use of bacteria-derived cyanocides is regarded as an environmentally friendly method for controlling cyanobacterial blooms, only a few studies have examined their potential impact on ecosystems. This study is the first to explore the response of particle-attached (PA) and free-living (FL) bacteria to the dynamics of microalgal communities induced by the biological cyanocide paucibactin A. The microalgal community dynamics were divided into two distinct phases [phase I (days 0-2) and phase II (days 3-7)]. In phase I, paucibactin A caused a sudden decrease in the cyanobacterial concentration. Phase II was characterized by increased growth of eukaryotic microalgae (Scenedesmus, Pediastrum, Selenastrum, and Coelastrum). The stability of the bacterial community and the contribution of stochastic processes to community assembly were more pronounced in phase II than in phase I. The microalgal dynamics triggered by paucibactin A coincided with the succession of the PA and FL bacterial communities. The lysis of cyanobacteria in phase I favored the growth of microbial organic matter degraders in both the PA (e.g., Aeromonas and Rheinheimera) and FL (e.g., Vogesella) bacterial communities. In phase II, Lacibacter, Phycisphaeraceae, and Hydrogenophaga in the PA bacterial community and Lacibacter, Peredibacter, and Prosthecobacter in the FL bacterial community showed increased relative abundances. Overall, the FL bacterial community exhibited greater sensitivity to the two sequential processes compared with the PA bacterial community. These results highlight the need for studies evaluating the impact of biological cyanocides on aquatic ecosystems when used to control natural cyanobacterial blooms.
Collapse
Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yuna Shin
- Water Quality Assessment Research Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Kyunghyun Kim
- Water Quality Assessment Research Division, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| |
Collapse
|
2
|
Wiley KS, Gregg AM, Fox MM, Lagishetty V, Sandman CA, Jacobs JP, Glynn LM. Contact with caregivers is associated with composition of the infant gastrointestinal microbiome in the first 6 months of life. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24858. [PMID: 37804008 PMCID: PMC10922139 DOI: 10.1002/ajpa.24858] [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: 08/18/2023] [Accepted: 09/24/2023] [Indexed: 10/08/2023]
Abstract
OBJECTIVES Little is known about how physical contact at birth and early caregiving environments influence the colonization of the infant gastrointestinal microbiome. We investigated how infant contact with caregivers at birth and within the first 2 weeks of life relates to the composition of the gastrointestinal microbiome in a sample of U.S. infants (n = 60). METHODS Skin-to-skin and physical contact with caregivers at birth and early caregiving environments were surveyed at 2 weeks postpartum. Stool samples were collected from infants at 2 weeks, 2, 6, and 12 months of age and underwent 16S rRNA sequencing as a proxy for the gastrointestinal microbiome. Associations between early caregiving environments and alpha and beta diversity, and differential abundance of bacteria at the genus level were assessed using PERMANOVA, and negative binomial mixed models in DEseq2. RESULTS Time in physical contact with caregivers explained 10% of variation in beta diversity at 2 weeks' age. The number of caregivers in the first few weeks of life explained 9% of variation in beta diversity at 2 weeks and the number of individuals in physical contact at birth explained 11% of variation in beta diversity at 6 months. Skin-to-skin contact on the day of birth was positively associated with the abundance of eight genera. Infants held for by more individuals had greater abundance of eight genera. DISCUSSION Results reveal a potential mechanism (skin-to-skin and physical contact) by which caregivers influence the infant gastrointestinal microbiome. Our findings contribute to work exploring the social transmission of microbes.
Collapse
Affiliation(s)
- Kyle S Wiley
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Andrew M Gregg
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Molly M Fox
- Department of Anthropology, UCLA, Los Angeles, California, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, California, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Curt A Sandman
- Department of Psychiatry and Human Behavior, UC Irvine, Irvine, California, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, California, USA
| | - Laura M Glynn
- Department of Psychology, Chapman University, Orange, California, USA
| |
Collapse
|
3
|
Pei L, Ye S, Xie L, Zhou P, He L, Yang S, Ding X, Yuan H, Dai T, Laws EA. Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China. Front Microbiol 2024; 15:1347821. [PMID: 38601935 PMCID: PMC11004437 DOI: 10.3389/fmicb.2024.1347821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.
Collapse
Affiliation(s)
- Lixin Pei
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Siyuan Ye
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Liujuan Xie
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Pan Zhou
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Lei He
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Shixiong Yang
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xigui Ding
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hongming Yuan
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Edward A. Laws
- Department of Environmental Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA, United States
| |
Collapse
|
4
|
Liu J, Wang J, Zhang M, Wang X, Guo P, Li Q, Ren J, Wei Y, Wu T, Chai B. Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170386. [PMID: 38280613 DOI: 10.1016/j.scitotenv.2024.170386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.
Collapse
Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiayi Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Xue Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Ping Guo
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Qianru Li
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Jiali Ren
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Yuqi Wei
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, GA 30460-8042, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan 030006, China.
| |
Collapse
|
5
|
Gao Y, Li Y, Shang J, Zhang W. Temporal profiling of sediment microbial communities in the Three Gorges Reservoir Area discovered time-dissimilarity patterns and multiple stable states. WATER RESEARCH 2024; 252:121225. [PMID: 38309070 DOI: 10.1016/j.watres.2024.121225] [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: 09/11/2023] [Revised: 01/25/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
Microbial communities play vital roles in cycling nutrients and maintaining water quality in aquatic ecosystems. To better understand the dynamics of microbial communities and to pave way to effective ecological remediation, it's essential to reveal the temporal patterns of the communities and to identify their states. However, research exploring the dynamic changes of microbial communities needs a large amount of time-series data, which could be an extravagant requirement for a single study. In this research, we overcame this challenge by conducting a meta-analysis of years of accumulations of 16S rRNA high-throughput sequencing data from the Three Gorges Reservoir Area (TGRA), an ecological and environmental hotspot. For better understanding the microbial communities time-dissimilarity dynamics, three microbial communities time-dissimilarity patterns were hypothesized, and the linear pattern in the TGRA was validated. In addition, to explore the stability of microbial communities in the TGRA, two alternative stable states were revealed, and their differences in community richness, alpha diversity indices, community composition, ecological network topological properties, and metabolic functions were demonstrated. In short, two states of microbial communities showed distinct richness and alpha diversity indices, and the communities in one state were more dominated by Halomonas and Nitrosopumilaceae genera, facilitating nitrogen cycling metabolic processes; whilst the main genera of the other state were Bathyarchaeia and Methanosaeta, which favored methane-related metabolism. Moreover, different studies and environmental differences between mainstream and tributaries were attributed as the potential inducing factors of the state division. Our study provides a comprehensive insight into the dynamics and stability of microbial communities in the TGRA, and a reference for future studies on microbial community dynamics.
Collapse
Affiliation(s)
- Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Jiahui Shang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| |
Collapse
|
6
|
Kempraj V, Auth J, Cha DH, Mason CJ. Impact of Larval Food Source on the Stability of the Bactrocera dorsalis Microbiome. MICROBIAL ECOLOGY 2024; 87:46. [PMID: 38407587 PMCID: PMC10896919 DOI: 10.1007/s00248-024-02352-9] [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: 11/14/2023] [Accepted: 01/22/2024] [Indexed: 02/27/2024]
Abstract
Bacterial symbionts are crucial to the biology of Bactrocera dorsalis. With larval diet (fruit host) being a key factor that determines microbiome composition and with B. dorsalis using more than 400 fruits as hosts, it is unclear if certain bacterial symbionts are preserved and are passed on to B. dorsalis progenies despite changes in larval diet. Here, we conducted a fly rearing experiment to characterize diet-induced changes in the microbiome of female B. dorsalis. In order to explicitly investigate the impacts of larval diet on the microbiome, including potential stable bacterial constituents of B. dorsalis, we performed 16S rRNA sequencing on the gut tissues of teneral female flies reared from four different host fruits (guava, mango, papaya, and rose apple) infested using a single cohort of wild B. dorsalis that emerged from tropical almond (mother flies). Although B. dorsalis-associated microbiota were predominantly shaped by the larval diet, some major bacterial species from the mother flies were retained in progenies raised on different larval diets. With some variation, Klebsiella (ASV 1 and 2), Morganella (ASV 3), and Providencia (ASV 6) were the major bacterial symbionts that were stable and made up 0.1-80% of the gut and ovipositor microbiome of female teneral flies reared on different host fruits. Our results suggest that certain groups of bacteria are stably associated with female B. dorsalis across larval diets. These findings provide a basis for unexplored research on symbiotic bacterial function in B. dorsalis and may aid in the development of novel management techniques against this devastating pest of horticultural importance.
Collapse
Affiliation(s)
- Vivek Kempraj
- USDA-ARS, Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA
- College of Tropical Agriculture and Human Resources, Komohana Research and Extension Center, University of Hawai'i, Hilo, HI, 96720, USA
| | - Jean Auth
- USDA-ARS, Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA
| | - Dong H Cha
- USDA-ARS, Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA.
| | - Charles J Mason
- USDA-ARS, Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K Inouye US Pacific Basin Agriculture Research Center, Hilo, HI, 96720, USA.
| |
Collapse
|
7
|
Sarkar A, McInroy CJA, Harty S, Raulo A, Ibata NGO, Valles-Colomer M, Johnson KVA, Brito IL, Henrich J, Archie EA, Barreiro LB, Gazzaniga FS, Finlay BB, Koonin EV, Carmody RN, Moeller AH. Microbial transmission in the social microbiome and host health and disease. Cell 2024; 187:17-43. [PMID: 38181740 PMCID: PMC10958648 DOI: 10.1016/j.cell.2023.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024]
Abstract
Although social interactions are known to drive pathogen transmission, the contributions of socially transmissible host-associated mutualists and commensals to host health and disease remain poorly explored. We use the concept of the social microbiome-the microbial metacommunity of a social network of hosts-to analyze the implications of social microbial transmission for host health and disease. We investigate the contributions of socially transmissible microbes to both eco-evolutionary microbiome community processes (colonization resistance, the evolution of virulence, and reactions to ecological disturbance) and microbial transmission-based processes (transmission of microbes with metabolic and immune effects, inter-specific transmission, transmission of antibiotic-resistant microbes, and transmission of viruses). We consider the implications of social microbial transmission for communicable and non-communicable diseases and evaluate the importance of a socially transmissible component underlying canonically non-communicable diseases. The social transmission of mutualists and commensals may play a significant, under-appreciated role in the social determinants of health and may act as a hidden force in social evolution.
Collapse
Affiliation(s)
- Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Cameron J A McInroy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Siobhán Harty
- Independent, Tandy Court, Spitalfields, Dublin, Ireland
| | - Aura Raulo
- Department of Biology, University of Oxford, Oxford, UK; Department of Computing, University of Turku, Turku, Finland
| | - Neil G O Ibata
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mireia Valles-Colomer
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Katerina V-A Johnson
- Institute of Psychology, Leiden University, Leiden, the Netherlands; Department of Psychiatry, University of Oxford, Oxford, UK
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph Henrich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Francesca S Gazzaniga
- Molecular Pathology Unit, Cancer Center, Massachusetts General Hospital Research Institute, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
8
|
Dong W, Ricker N, Holman DB, Johnson TA. Meta-analysis reveals the predictable dynamic development of the gut microbiota in commercial pigs. Microbiol Spectr 2023; 11:e0172223. [PMID: 37815394 PMCID: PMC10715009 DOI: 10.1128/spectrum.01722-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/24/2023] [Indexed: 10/11/2023] Open
Abstract
IMPORTANCE The swine gut microbiome undergoes an age-dependent assembly pattern with a developmental phase at early ages and a stabilization phase at later ages. Shorter time intervals and a wider range of data sources provided a clearer understanding of the gut microbiota colonization and succession and their associations with pig growth and development. The rapidly changing microbiota of suckling and weaning pigs implies potential time targets for growth and health regulation through gut microbiota manipulation. Since swine gut microbiota development is predictable, swine microbiota age can be calculated and compared between animal treatment groups rather than relying only on static time-matched comparisons.
Collapse
Affiliation(s)
- Wenxuan Dong
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Nicole Ricker
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Timothy A. Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|
9
|
Le VV, Kang M, Ko SR, Jeong S, Park CY, Lee JJ, Choi IC, Oh HM, Ahn CY. Dynamic response of bacterial communities to Microcystis blooms: A three-year study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:165888. [PMID: 37544456 DOI: 10.1016/j.scitotenv.2023.165888] [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: 05/26/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023]
Abstract
Although nutrient availability is widely recognized as the driving force behind Microcystis blooms, identifying the microorganisms that play a pivotal role in their formation is a challenging task. Our understanding of the contribution of bacterial communities to the development of Microcystis blooms remains incomplete, despite the fact that the relationship between Microcystis and bacterial communities has been extensively investigated. Most studies have focused on their interaction for a single year rather than for multiple years. To determine key bacteria crucial for the formation of Microcystis blooms, we collected samples from three sites in the Daechung Reservoir (Chuso, Hoenam, and Janggye) over three years (2017, 2019, and 2020). Our results indicated that Microcystis bloom-associated bacterial communities were more conserved across stations than across years. Bacterial communities could be separated into modules corresponding to the different phases of Microcystis blooms. Dolichospermum and Aphanizomenon belonged to the same module, whereas the module of Microcystis was distinct. The microbial recurrent association network (MRAN) showed that amplicon sequence variants (ASVs) directly linked to Microcystis belonged to Pseudanabaena, Microscillaceae, Sutterellaceae, Flavobacterium, Candidatus Aquiluna, Bryobacter, and DSSD61. These ASVs were also identified as key indicators of the bloom stage, indicating that they were fundamental biological elements in the development of Microcystis blooms. Overall, our study highlights that, although bacterial communities change annually, they continue to share core ASVs that may be crucial for the formation and maintenance of Microcystis blooms.
Collapse
Affiliation(s)
- Ve Van Le
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seonah Jeong
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jay Jung Lee
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk 29027, Republic of Korea
| | - In-Chan Choi
- Geum River Environment Research Center, National Institute of Environmental Research, Chungbuk 29027, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea.
| |
Collapse
|
10
|
Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice. Cell Rep 2023; 42:113233. [PMID: 38510311 PMCID: PMC10954246 DOI: 10.1016/j.celrep.2023.113233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers in Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no-MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.
Collapse
Affiliation(s)
- Rebecca H. Gellman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolé cules Biologiques, INRAE, CNRS, Aix-Marseille Université, Marseille, France
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
- Lead contact
| |
Collapse
|
11
|
Stochastic Processes Drive the Assembly and Metabolite Profiles of Keystone Taxa during Chinese Strong-Flavor Baijiu Fermentation. Microbiol Spectr 2023:e0510322. [PMID: 36916915 PMCID: PMC10101002 DOI: 10.1128/spectrum.05103-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Multispecies communities participate in the fermentation of Chinese strong-flavor Baijiu (CSFB), and the metabolic activity of the dominant and keystone taxa is key to the flavor quality of the final product. However, their roles in metabolic function and assembly processes are still not fully understood. Here, we identified the variations in the metabolic profiles of dominant and keystone taxa and characterized their community assembly using 16S rRNA and internal transcribed spacer (ITS) gene amplicon and metatranscriptome sequencing. We demonstrate that CSFB fermentations with distinct metabolic profiles display distinct microbial community compositions and microbial network complexities and stabilities. We then identified the dominant taxa (Limosilactobacillus fermentum, Kazachstania africana, Saccharomyces cerevisiae, and Pichia kudriavzevii) and the keystone ecological cluster (module 0, affiliated mainly with Thermoascus aurantiacus, Weissella confusa, and Aspergillus amstelodami) that cause changes in metabolic profiles. Moreover, we highlight that the alpha diversity of keystone taxa contributes to changes in metabolic profiles, whereas dominant taxa exert their influence on metabolic profiles by virtue of their relative abundance. Additionally, our results based on the normalized stochasticity ratio (NST) index and the neutral model revealed that stochastic and deterministic processes together shaped CSFB microbial community assemblies. Stochasticity and environmental selection structure the keystone and dominant taxa differently. This study provides new insights into understanding the relationships between microbial communities and their metabolic functions. IMPORTANCE From an ecological perspective, keystone taxa in microbial networks with high connectivity have crucial roles in community assembly and function. We used CSFB fermentation as a model system to study the ecological functions of dominant and keystone taxa at the metabolic level. We show that both dominant taxa (e.g., those taxa that have the highest relative abundances) and keystone taxa (e.g., those taxa with the most cooccurrences) affected the resulting flavor profiles. Moreover, our findings established that stochastic processes were dominant in shaping the communities of keystone taxa during CSFB fermentation. This result is striking as it suggests that although the controlled conditions in the fermentor can determine the dominant taxa, the uncontrolled rare keystone taxa in the microbial community can alter the resulting flavor profiles. This important insight is vital for the development of potential manipulation strategies to improve the quality of CSFB through the regulation of keystone species.
Collapse
|
12
|
Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531063. [PMID: 36945614 PMCID: PMC10028851 DOI: 10.1101/2023.03.08.531063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers of Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.
Collapse
Affiliation(s)
- Rebecca H Gellman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, INRAE, CNRS, Aix-Marseille Université, Marseille, France
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
13
|
Le VV, Ko SR, Kang M, Park CY, Lee SA, Oh HM, Ahn CY. The cyanobactericidal bacterium Paucibacter aquatile DH15 caused the decline of Microcystis and aquatic microbial community succession: A mesocosm study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119849. [PMID: 35952989 DOI: 10.1016/j.envpol.2022.119849] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Microcystis blooms pose a major threat to the quality of drinking water. Cyanobactericidal bacteria have attracted much attention in the research community as a vehicle for controlling Microcystis blooms because of their ecological safety. Nonetheless, most studies on cyanobactericidal bacteria have been conducted on a laboratory scale but have not been scaled-up as field experiments. Thus, our understanding of the microbial response to cyanobactericidal bacteria in natural ecosystems remains elusive. Herein, we applied Paucibacter aquatile DH15 to control Microcystis blooms in a 1000 L mesocosm experiment and demonstrated its potential with the following results: (1) DH15 reduced Microcystis cell density by 90.7% within two days; (2) microcystins released by Microcystis death decreased to the control level in four days; (3) during the cyanobactericidal processes, the physicochemical parameters of water quality remained safe for other aquatic organisms; and (4) the cyanobactericidal processes promoted the growth of eukaryotic microalgae, replacing cyanobacteria. The cyanobactericidal processes accelerated turnover rates, decreased stability, and altered the functional profile of the microbial community. Network analysis demonstrated that this process resulted in more complex interactions between microbes. Overall, our findings suggest that strain DH15 could be considered a promising candidate for controlling Microcystis blooms in an eco-friendly manner.
Collapse
Affiliation(s)
- Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - So-Ra Ko
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Mingyeong Kang
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sang-Ah Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea; Environmental Safety Groups, Korea Institute of Science and Technology (KIST) Europe, Saarbrücken 66123, Germany
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea.
| |
Collapse
|
14
|
Xiong X, Loo SL, Tanaka MM. Gut mutualists can persist in host populations despite low fidelity of vertical transmission. EVOLUTIONARY HUMAN SCIENCES 2022; 4:e41. [PMID: 37588926 PMCID: PMC10426022 DOI: 10.1017/ehs.2022.38] [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: 12/21/2021] [Revised: 06/30/2022] [Accepted: 08/09/2022] [Indexed: 11/07/2022] Open
Abstract
Humans harbour diverse microbial communities, and this interaction has fitness consequences for hosts and symbionts. Understanding the mechanisms that preserve host-symbiont association is an important step in studying co-evolution between humans and their mutualist microbial partners. This association is promoted by vertical transmission, which is known to be imperfect. It is unclear whether host-microbial associations can generally be maintained despite 'leaky' vertical transmission. Cultural practices of the host are expected to be important in bacterial transmission as they influence the host's interaction with other individuals and with the environment. There is a need to understand whether and how cultural practices affect host-microbial associations. Here, we develop a mathematical model to identify the conditions under which the mutualist can persist in a population where vertical transmission is imperfect. We show with this model that several factors compensate for imperfect vertical transmission, namely, a selective advantage to the host conferred by the mutualist, horizontal transmission of the mutualist through an environmental reservoir and transmission of a cultural practice that promotes microbial transmission. By making the host-microbe association more likely to persist in the face of leaky vertical transmission, these factors strengthen the association which in turn enables host-mutualist co-evolution.
Collapse
Affiliation(s)
- Xiyan Xiong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sara L. Loo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mark M. Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
15
|
Ojima MN, Jiang L, Arzamasov AA, Yoshida K, Odamaki T, Xiao J, Nakajima A, Kitaoka M, Hirose J, Urashima T, Katoh T, Gotoh A, van Sinderen D, Rodionov DA, Osterman AL, Sakanaka M, Katayama T. Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides. THE ISME JOURNAL 2022; 16:2265-2279. [PMID: 35768643 PMCID: PMC9381805 DOI: 10.1038/s41396-022-01270-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022]
Abstract
Bifidobacteria are among the first colonizers of the infant gut, and human milk oligosaccharides (HMOs) in breastmilk are instrumental for the formation of a bifidobacteria-rich microbiota. However, little is known about the assembly of bifidobacterial communities. Here, by applying assembly theory to a community of four representative infant-gut associated Bifidobacterium species that employ varied strategies for HMO consumption, we show that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis, two avid HMO consumers, dominate through inhibitory priority effects. On the other hand, Bifidobacterium breve, a species with limited HMO-utilization ability, can benefit from facilitative priority effects and dominates by utilizing fucose, an HMO degradant not utilized by the other bifidobacterial species. Analysis of publicly available breastfed infant faecal metagenome data showed that the observed trends for B. breve were consistent with our in vitro data, suggesting that priority effects may have contributed to its dominance. Our study highlights the importance and history dependency of initial community assembly and its implications for the maturation trajectory of the infant gut microbiota.
Collapse
Affiliation(s)
- Miriam N Ojima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Keisuke Yoshida
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Toshitaka Odamaki
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Jinzhong Xiao
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Aruto Nakajima
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | - Junko Hirose
- School of Human Cultures, The University of Shiga Prefecture, Hikone, Shiga, Japan
- Department of Food and Nutrition, Kyoto Women's University, Kyoto, Japan
| | - Tadasu Urashima
- Department of Food and Life Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, Food Science Building, University College Cork, Cork, Ireland
| | - Dmitry A Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| |
Collapse
|
16
|
Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng XD, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science 2022; 376:1220-1223. [PMID: 35679413 PMCID: PMC9894631 DOI: 10.1126/science.abj2972] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.
Collapse
Affiliation(s)
- Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew M. Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Wastyk
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Holmes
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Corresponding author:
| |
Collapse
|
17
|
Mangola SM, Lund JR, Schnorr SL, Crittenden AN. Ethical microbiome research with Indigenous communities. Nat Microbiol 2022; 7:749-756. [PMID: 35577973 DOI: 10.1038/s41564-022-01116-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/31/2022] [Indexed: 11/10/2022]
Abstract
Human-microbiome interactions have been associated with evolutionary, cultural and environmental processes. With clinical applications of microbiome research now feasible, it is crucial that the science conducted, particularly among Indigenous communities, adheres to principles of inclusion. This necessitates a transdisciplinary dialogue to decide how biological samples are collected and who benefits from the research and any derived products. As a group of scholars working at the interface of biological and social science, we offer a candid discussion of the lessons learned from our own research and introduce one approach to carry out ethical microbiome research with Indigenous communities.
Collapse
Affiliation(s)
- Shani Msafiri Mangola
- Indigenous Peoples Law and Policy Program, James E. Rogers College of Law, University of Arizona, Tucson, AZ, USA.,Olanakwe Community Fund (USA), Boulder City, NV, USA.,Olanakwe Community Fund (TZ), Mang'ola Ward, Karatu, Tanzania
| | - Justin R Lund
- Center for the Ethics of Indigenous Genomics Research, University of Oklahoma, Norman, OK, USA.,Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Alyssa N Crittenden
- Olanakwe Community Fund (USA), Boulder City, NV, USA. .,Laboratory of Nutrition and Reproduction, Department of Anthropology, University of Nevada, Las Vegas, NV, USA.
| |
Collapse
|
18
|
Chen DW, Garud NR. Rapid evolution and strain turnover in the infant gut microbiome. Genome Res 2022; 32:1124-1136. [PMID: 35545448 DOI: 10.1101/gr.276306.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
While the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from >700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from that of adults. We find evidence for more than 10-fold increase in the rate of evolution and strain turnover in the infant gut compared to healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.
Collapse
Affiliation(s)
- Daisy W Chen
- University of California, Los Angeles, University of California, San Diego
| | | |
Collapse
|
19
|
Caspani G, Green M, Swann JR, Foster JA. Microbe-Immune Crosstalk: Evidence That T Cells Influence the Development of the Brain Metabolome. Int J Mol Sci 2022; 23:3259. [PMID: 35328680 PMCID: PMC8952415 DOI: 10.3390/ijms23063259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/06/2022] [Accepted: 03/10/2022] [Indexed: 11/21/2022] Open
Abstract
Cross-talk between the immune system and the brain is essential to neuronal development, neuronal excitability, neuroplasticity, and neurotransmission. Gut microbiota are essential to immune system development and immune function; hence, it is essential to consider more broadly the microbiota-immune-brain axis in neurodevelopment. The gut, brain, and microbial metabolomes obtained from C57Bl/6 and T-cell-deficient mice across four developmental timepoints (postnatal day 17, 24, 28, and 84) were studied by 1H NMR spectroscopy. 16S rRNA gene sequencing was performed on cecal and fecal samples. In the absence of T-cells, the developmental trajectory of the gut microbiota and of the host's metabolic profile was altered. The novel insights from this work include (1) the requirement of functional T-cells for the normal trajectory of microbiotal development and the metabolic maturation of the supra-organism, (2) the potential role for Muribaculaceae taxa in modulating the cecal availability of metabolites previously implicated with a role in the gut-brain axis in T-cell deficient mice, and (3) the impact of T-cell-deficiency on central levels of neuroactive metabolites.
Collapse
Affiliation(s)
- Giorgia Caspani
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK; (G.C.); (J.R.S.)
| | - Miranda Green
- Department of Psychiatry & Behavioral Neurosciences, McMaster University, Hamilton, ON L8S 4L8, Canada;
| | - Jonathan R. Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW7 2AZ, UK; (G.C.); (J.R.S.)
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Jane A. Foster
- Department of Psychiatry & Behavioral Neurosciences, McMaster University, Hamilton, ON L8S 4L8, Canada;
- St. Joseph’s Healthcare, Hamilton, ON L8N 4A6, Canada
- Centre for Depression and Suicide Studies, St. Michael’s Hospital, Toronto, ON M5B 1A6, Canada
| |
Collapse
|
20
|
Er YX, Lee SC, Than LTL, Muslim A, Leong KF, Kwan Z, Mohd Sayed I, Lim YAL. Tinea Imbricata among the Indigenous Communities: Current Global Epidemiology and Research Gaps Associated with Host Genetics and Skin Microbiota. J Fungi (Basel) 2022; 8:202. [PMID: 35205956 PMCID: PMC8880274 DOI: 10.3390/jof8020202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Tinea imbricata is a unique fungal skin disease that mostly affects indigenous populations in Southeast Asia, Oceania, and Central and South America. The control and management of this disease among these communities are challenging given their remote locations, certain traditional practices, and severe malnutrition status. To date, there are only a handful of reports published globally, which highlights the need for a more holistic approach in addressing this skin disease. Several bodies of evidence and reports have shown that host genetic factors have a profound influence on the pathogenesis of tinea imbricata, while skin microbiota is touted to have a role in the pathogenesis of the disease. However, there are limited studies of how host genetics and skin microbiota impact disease susceptibility in the host. To improve the understanding of this disease and to find possible long-term effective treatment among the affected indigenous communities, a comprehensive literature review is needed. Hence, this review paper aims to present the current status of tinea imbricata among the indigenous communities, together with published findings on the possible underlying reasons for its specific distribution among these communities, particularly on the ways in which host skin microbiota and host genetics affect occurrence and disease patterns. This information provides valuable insights for future research by highlighting the current knowledge gaps in these areas.
Collapse
Affiliation(s)
- Yi Xian Er
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Soo Ching Lee
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Leslie Thian-Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Azdayanti Muslim
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA (Sungai Buloh Campus), Sungai Buloh 47000, Malaysia;
- Institute for Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA (Sungai Buloh Campus), Sungai Buloh 47000, Malaysia
| | - Kin Fon Leong
- Pediatric Institute, Kuala Lumpur General Hospital, Kuala Lumpur 50586, Malaysia;
| | - Zhenli Kwan
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Izandis Mohd Sayed
- Hospital Orang Asli (Aborigines) Gombak, Jalan Pahang Lama, Gombak 53100, Malaysia;
| | - Yvonne Ai-Lian Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Centre for Malaysian Indigenous Studies, Universiti Malaya, Jalan 16/4, Seksyen 16, Petaling Jaya 46350, Malaysia
| |
Collapse
|
21
|
Microbiome assembly in The Gambia. Nat Microbiol 2022; 7:18-19. [PMID: 34972823 DOI: 10.1038/s41564-021-01036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
22
|
Fox M, Lee SM, Wiley KS, Lagishetty V, Sandman CA, Jacobs JP, Glynn LM. Development of the infant gut microbiome predicts temperament across the first year of life. Dev Psychopathol 2021; 34:1-12. [PMID: 34108055 PMCID: PMC9463039 DOI: 10.1017/s0954579421000456] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Perturbations to the gut microbiome are implicated in altered neurodevelopmental trajectories that may shape life span risk for emotion dysregulation and affective disorders. However, the sensitive periods during which the microbiome may influence neurodevelopment remain understudied. We investigated relationships between gut microbiome composition across infancy and temperament at 12 months of age. In 67 infants, we examined if gut microbiome composition assessed at 1-3 weeks, 2, 6, and 12 months of age was associated with temperament at age 12 months. Stool samples were sequenced using the 16S Illumina MiSeq platform. Temperament was assessed using the Infant Behavior Questionnaire-Revised (IBQ-R). Beta diversity at age 1-3 weeks was associated with surgency/extraversion at age 12 months. Bifidobacterium and Lachnospiraceae abundance at 1-3 weeks of age was positively associated with surgency/extraversion at age 12 months. Klebsiella abundance at 1-3 weeks was negatively associated with surgency/extraversion at 12 months. Concurrent composition was associated with negative affectivity at 12 months, including a positive association with Ruminococcus-1 and a negative association with Lactobacillus. Our findings support a relationship between gut microbiome composition and infant temperament. While exploratory due to the small sample size, these results point to early and late infancy as sensitive periods during which the gut microbiome may exert effects on neurodevelopment.
Collapse
Affiliation(s)
- Molly Fox
- Department of Anthropology, UCLA, Los Angeles, CA, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, CA, USA
| | - S. Melanie Lee
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Kyle S. Wiley
- Department of Anthropology, UCLA, Los Angeles, CA, USA
- Department of Psychiatry & Biobehavioral Sciences, UCLA, Los Angeles, CA, USA
| | - Venu Lagishetty
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Curt A. Sandman
- Department of Psychiatry and Human Behavior, UC Irvine, Irvine, CA, USA
| | - Jonathan P. Jacobs
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Laura M. Glynn
- Department of Psychology, Chapman University, Orange, CA, USA
| |
Collapse
|
23
|
Abstract
Human guts are colonized at birth by a limited set of microbes that gradually increases in diversity throughout infancy. A new study reports the opposite pattern in infant chimpanzees, raising questions about how host-microbiota relationships have changed during ape evolution.
Collapse
Affiliation(s)
- Daniel D Sprockett
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - Andrew H Moeller
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA.
| |
Collapse
|
24
|
Laursen MF, Bahl MI, Licht TR. Settlers of our inner surface - Factors shaping the gut microbiota from birth to toddlerhood. FEMS Microbiol Rev 2021; 45:6081092. [PMID: 33428723 PMCID: PMC8371275 DOI: 10.1093/femsre/fuab001] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
During the first 3 years of life, the microbial ecosystem within the human gut undergoes a process that is unlike what happens in this ecosystem at any other time of our life. This period in time is considered a highly important developmental window, where the gut microbiota is much less resilient and much more responsive to external and environmental factors than seen in the adult gut. While advanced bioinformatics and clinical correlation studies have received extensive focus within studies of the human microbiome, basic microbial growth physiology has attracted much less attention, although it plays a pivotal role to understand the developing gut microbiota during early life. In this review, we will thus take a microbial ecology perspective on the analysis of factors that influence the temporal development of the infant gut microbiota. Such factors include sources of microbes that seed the intestinal environment, physico-chemical (abiotic) conditions influencing microbial growth and the availability of nutrients needed by the intestinal microbes.
Collapse
Affiliation(s)
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, DK-2800 Kgs. Lyngby
| |
Collapse
|