1
|
Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
Collapse
Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
2
|
Wu R, Davison MR, Nelson WC, Smith ML, Lipton MS, Jansson JK, McClure RS, McDermott JE, Hofmockel KS. Hi-C metagenome sequencing reveals soil phage-host interactions. Nat Commun 2023; 14:7666. [PMID: 37996432 PMCID: PMC10667309 DOI: 10.1038/s41467-023-42967-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.
Collapse
Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michelle R Davison
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William C Nelson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Montana L Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan S McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Department of Agronomy, Iowa State University, Ames, IA, USA.
| |
Collapse
|
3
|
Bhattacharjee A, Velickovic D, Richardson JA, Couvillion SP, Vandergrift GW, Qafoku O, Taylor MJ, Jansson JK, Hofmockel K, Anderton CR. Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot. mBio 2023; 14:e0095623. [PMID: 37655873 PMCID: PMC10653886 DOI: 10.1128/mbio.00956-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Fungal species are foundational members of soil ecosystems with vital contributions that support interspecies resource translocation. The minute details of these biogeochemical processes are poorly investigated. Here, we addressed this knowledge gap by probing fungal growth in a novel mineral-doped soil micromodel platform using spatially-resolved imaging methodologies. We found that fungi uptake K from K-rich minerals using organic acids exuded in a distance-dependent manner from a carbon-rich hotspot. While identification of specific mechanisms within soil remains challenging, our findings demonstrate the significance of reduced complexity platforms such as the mineral-doped micromodel in probing biogeochemical processes. These findings provide visualization into hyphal uptake and transport of mineral-derived nutrients in a resource-limited environment.
Collapse
Affiliation(s)
- Arunima Bhattacharjee
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jocelyn A. Richardson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sneha P. Couvillion
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory W. Vandergrift
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Odeta Qafoku
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Michael J. Taylor
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Janet K. Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten Hofmockel
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| |
Collapse
|
4
|
Naasko KI, Naylor D, Graham EB, Couvillion SP, Danczak R, Tolic N, Nicora C, Fransen S, Tao H, Hofmockel KS, Jansson JK. Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry. mBio 2023; 14:e0175823. [PMID: 37728606 PMCID: PMC10653930 DOI: 10.1128/mbio.01758-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
IMPORTANCE Carbon is cycled through the air, plants, and belowground environment. Understanding soil carbon cycling in deep soil profiles will be important to mitigate climate change. Soil carbon cycling is impacted by water, plants, and soil microorganisms, in addition to soil mineralogy. Measuring biotic and abiotic soil properties provides a perspective of how soil microorganisms interact with the surrounding chemical environment. This study emphasizes the importance of considering biotic interactions with inorganic and oxidizable soil carbon in addition to total organic carbon in carbonate-containing soils for better informing soil carbon management decisions.
Collapse
Affiliation(s)
- Katherine I. Naasko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Daniel Naylor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Emily B. Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sneha P. Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert Danczak
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Nikola Tolic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven Fransen
- Department of Crop and Soil Sciences, Washington State University, Prosser, Washington, USA
| | - Haiying Tao
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, Connecticut, USA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| |
Collapse
|
5
|
Smith ML, Weitz KK, Thompson AM, Jansson JK, Hofmockel KS, Lipton MS. Real-Time and Rapid Respiratory Response of the Soil Microbiome to Moisture Shifts. Microorganisms 2023; 11:2630. [PMID: 38004642 PMCID: PMC10673078 DOI: 10.3390/microorganisms11112630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 11/26/2023] Open
Abstract
Microbial response to changing environmental factors influences the fate of soil organic carbon, and drought has been shown to affect microbial metabolism and respiration. We hypothesized that the access of microbes to different carbon pools in response to dry-rewet events occurs sequentially at different rates. We amended desiccated soils with 13C-labeled glucose and measured the rates of 12CO2 and 13CO2 respiration in real time after rewetting. Using these differentiated 12CO2 and 13CO2 respiration rate soils after rewetting, we were able to deduce when microbes are accessing different pools of carbon. Immediately upon rewetting, respiration of 12CO2 occurred first, with negligible 13CO2 respiration. Appreciable metabolism and respiration of the added 13C glucose did not occur until 15 min after rewetting. We conclude that, while all carbon pools are being accessed in the first 9 h after rewetting, the rate and timing at which new and existing carbon pools are being accessed varies. Within this study, using stable isotope-labeled substrates to discern which carbon pools are metabolized first uniquely illustrates how microorganisms access different carbon pools which has implications into understanding how carbon metabolism can further affect climate, carbon sequestration, and soil health.
Collapse
Affiliation(s)
| | | | | | | | | | - Mary S. Lipton
- Pacific Northwest National Laboratory, Richland, WA 99354, USA; (M.L.S.); (K.K.W.); (J.K.J.); (K.S.H.)
| |
Collapse
|
6
|
Jansson JK. Microorganisms, climate change, and the Sustainable Development Goals: progress and challenges. Nat Rev Microbiol 2023; 21:622-623. [PMID: 37500766 DOI: 10.1038/s41579-023-00953-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Affiliation(s)
- Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| |
Collapse
|
7
|
Abstract
Soil viruses are highly abundant and have important roles in the regulation of host dynamics and soil ecology. Climate change is resulting in unprecedented changes to soil ecosystems and the life forms that reside there, including viruses. In this Review, we explore our current understanding of soil viral diversity and ecology, and we discuss how climate change (such as extended and extreme drought events or more flooding and altered precipitation patterns) is influencing soil viruses. Finally, we provide our perspective on future research needs to better understand how climate change will impact soil viral ecology.
Collapse
Affiliation(s)
- Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
8
|
Couvillion SP, Danczak RE, Naylor D, Smith ML, Stratton KG, Paurus VL, Bloodsworth KJ, Farris Y, Schmidt DJ, Richardson RE, Bramer LM, Fansler SJ, Nakayasu ES, McDermott JE, Metz TO, Lipton MS, Jansson JK, Hofmockel KS. Rapid remodeling of the soil lipidome in response to a drying-rewetting event. Microbiome 2023; 11:34. [PMID: 36849975 PMCID: PMC9969633 DOI: 10.1186/s40168-022-01427-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/15/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microbiomes contribute to multiple ecosystem services by transforming organic matter in the soil. Extreme shifts in the environment, such as drying-rewetting cycles during drought, can impact the microbial metabolism of organic matter by altering microbial physiology and function. These physiological responses are mediated in part by lipids that are responsible for regulating interactions between cells and the environment. Despite this critical role in regulating the microbial response to stress, little is known about microbial lipids and metabolites in the soil or how they influence phenotypes that are expressed under drying-rewetting cycles. To address this knowledge gap, we conducted a soil incubation experiment to simulate soil drying during a summer drought of an arid grassland, then measured the response of the soil lipidome and metabolome during the first 3 h after wet-up. RESULTS Reduced nutrient access during soil drying incurred a replacement of membrane phospholipids, resulting in a diminished abundance of multiple phosphorus-rich membrane lipids. The hot and dry conditions increased the prevalence of sphingolipids and lipids containing long-chain polyunsaturated fatty acids, both of which are associated with heat and osmotic stress-mitigating properties in fungi. This novel finding suggests that lipids commonly present in eukaryotes such as fungi may play a significant role in supporting community resilience displayed by arid land soil microbiomes during drought. As early as 10 min after rewetting dry soil, distinct changes were observed in several lipids that had bacterial signatures including a rapid increase in the abundance of glycerophospholipids with saturated and short fatty acid chains, prototypical of bacterial membrane lipids. Polar metabolites including disaccharides, nucleic acids, organic acids, inositols, and amino acids also increased in abundance upon rewetting. This rapid metabolic reactivation and growth after rewetting coincided with an increase in the relative abundance of firmicutes, suggesting that members of this phylum were positively impacted by rewetting. CONCLUSIONS Our study revealed specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. The drought-induced nutrient limitation was reflected in the lipidome and polar metabolome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long-chain polyunsaturated fatty acids in dry soil suggest that lipids likely play an important role in the drought tolerance of microbial taxa capable of synthesizing these lipids. An increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest a metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Video Abstract.
Collapse
Affiliation(s)
- Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert E Danczak
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dan Naylor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Montana L Smith
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kelly G Stratton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Vanessa L Paurus
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kent J Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuliya Farris
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Darren J Schmidt
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rachel E Richardson
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lisa M Bramer
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah J Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mary S Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- Department of Agronomy, Iowa State University, Ames, IA, USA.
| |
Collapse
|
9
|
Jansson JK. Soil viruses: Understudied agents of soil ecology. Environ Microbiol 2023; 25:143-146. [PMID: 36271323 PMCID: PMC10100255 DOI: 10.1111/1462-2920.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/21/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Janet K Jansson
- Department of Biosciences, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| |
Collapse
|
10
|
McClure R, Farris Y, Danczak R, Nelson W, Song HS, Kessell A, Lee JY, Couvillion S, Henry C, Jansson JK, Hofmockel KS. Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes. mSystems 2022; 7:e0037222. [PMID: 36154140 PMCID: PMC9599572 DOI: 10.1128/msystems.00372-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 12/24/2022] Open
Abstract
Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomposition. Chitin was applied to a model soil consortium that we developed, "model soil consortium-2" (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders. A multiomics approach revealed how MSC-2 community-level processes during chitin decomposition differ from monocultures of the constituent species. Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. The members of MSC-2 were further evaluated via metatranscriptomics and community metabolomics. Intriguingly, the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products. Using a model soil consortium greatly increased our knowledge of how carbon is decomposed and metabolized in a community setting, showing that niche size, rather than species metabolic capacity, can drive success and that certain species become active carbon degraders only in the context of their surrounding community. These conclusions fill important knowledge gaps that are key to our understanding of community interactions that support carbon and nitrogen cycling in soil. IMPORTANCE The soil microbiome performs many functions that are key to ecology, agriculture, and nutrient cycling. However, because of the complexity of this ecosystem we do not know the molecular details of the interactions between microbial species that lead to these important functions. Here, we use a representative but simplified model community of bacteria to understand the details of these interactions. We show that certain species act as primary degraders of carbon sources and that the most successful species are likely those that can take the most advantage of breakdown products, not necessarily the primary degraders. We also show that a species phenotype, including whether it is a primary degrader or not, is driven in large part by the membership of the community it resides in. These conclusions are critical to a better understanding of the soil microbial interaction network and how these interactions drive central soil microbiome functions.
Collapse
Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Robert Danczak
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Aimee Kessell
- Department of Biological Systems Engineering, University of Nebraska—Lincoln, Lincoln, Nebraska, USA
| | - Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Henry
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, USA
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten S. Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| |
Collapse
|
11
|
Lee JY, Mitchell HD, Burnet MC, Wu R, Jenson SC, Merkley ED, Nakayasu ES, Nicora CD, Jansson JK, Burnum-Johnson KE, Payne SH. Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics. J Proteome Res 2022; 21:2023-2035. [PMID: 35793793 PMCID: PMC9361346 DOI: 10.1021/acs.jproteome.2c00334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Metaproteomics has
been increasingly utilized for high-throughput
characterization of proteins in complex environments and has been
demonstrated to provide insights into microbial composition and functional
roles. However, significant challenges remain in metaproteomic data
analysis, including creation of a sample-specific protein sequence
database. A well-matched database is a requirement for successful
metaproteomics analysis, and the accuracy and sensitivity of PSM identification
algorithms suffer when the database is incomplete or contains extraneous
sequences. When matched DNA sequencing data of the sample is unavailable
or incomplete, creating the proteome database that accurately represents
the organisms in the sample is a challenge. Here, we leverage a de novo peptide sequencing approach to identify the sample
composition directly from metaproteomic data. First, we created a
deep learning model, Kaiko, to predict the peptide sequences from
mass spectrometry data and trained it on 5 million peptide–spectrum
matches from 55 phylogenetically diverse bacteria. After training,
Kaiko successfully identified organisms from soil isolates and synthetic
communities directly from proteomics data. Finally, we created a pipeline
for metaproteome database generation using Kaiko. We tested the pipeline
on native soils collected in Kansas, showing that the de novo sequencing model can be employed as an alternative and complementary
method to construct the sample-specific protein database instead of
relying on (un)matched metagenomes. Our pipeline identified all highly
abundant taxa from 16S rRNA sequencing of the soil samples and uncovered
several additional species which were strongly represented only in
proteomic data.
Collapse
Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah C Jenson
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eric D Merkley
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
12
|
Jurelevicius D, Pereira RDS, da Mota FF, Cury JC, de Oliveira IC, Rosado AS, Mason OU, Jansson JK, Seldin L. Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica. Geobiology 2022; 20:98-111. [PMID: 34545693 DOI: 10.1111/gbi.12472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/28/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.
Collapse
Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael da Silva Pereira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Juliano C Cury
- Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Ivan Cardoso de Oliveira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
13
|
Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 2021; 9:208. [PMID: 34663463 PMCID: PMC8522061 DOI: 10.1186/s40168-021-01154-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). RESULTS We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. CONCLUSIONS Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.
Collapse
Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jose Liquet-Gonzalez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark P Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| |
Collapse
|
14
|
Wu R, Davison MR, Gao Y, Nicora CD, Mcdermott JE, Burnum-Johnson KE, Hofmockel KS, Jansson JK. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun Biol 2021; 4:992. [PMID: 34446837 PMCID: PMC8390657 DOI: 10.1038/s42003-021-02514-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/18/2021] [Indexed: 02/07/2023] Open
Abstract
Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that higher soil moisture increased transcription of a subset of DNA viruses. Metaproteome data validated that the specific viral transcripts were translated into proteins, including chaperonins known to be essential for virion replication and assembly. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. The soil also had a high abundance of RNA viruses, with highest representation of Reoviridae. Leviviridae were the most diverse RNA viruses in the samples, with higher amounts in wet soil. This study demonstrates that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses.
Collapse
Affiliation(s)
- Ruonan Wu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Michelle R Davison
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E Mcdermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| |
Collapse
|
15
|
Neal AL, Hughes D, Clark IM, Jansson JK, Hirsch PR. Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity. mSystems 2021; 6:e0105620. [PMID: 34042469 PMCID: PMC8269249 DOI: 10.1128/msystems.01056-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/29/2021] [Indexed: 11/20/2022] Open
Abstract
How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes, resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements, and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic (press) disturbance of the magnitude of organic carbon inputs with acute (pulse) effects of physical disturbance by tillage and chemical disturbance due to inorganic fertilization and pesticide application. We show that because of the variety of ways it can be assessed, biodiversity-here based on microbial small subunit rRNA gene phylotypes-does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with rRNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea, and fungi do not share a common response to land management change, and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately. IMPORTANCE Changes in soil microbiome diversity and function brought about by land management are predicted to influence a range of environmental services provided by soil, including provision of food and clean water. However, opportunities to compare the long-term effects of combinations of stresses imposed by different management approaches are limited. We exploit a globally unique 50-year field experiment, demonstrating that soil management practices alter microbiome diversity, community traits, and assembly. Grassland soil microbiomes are dominated by fewer-but phylogenetically more diverse-prokaryote phylotypes which sustain larger genomes than microbiomes in arable or bare fallow soil maintained free of plants. Dominant fungi in grassland soils are less phylogenetically diverse than those in arable or fallow soils. Soil tillage increases stochastic processes in microbiome assembly: this, combined with reduced plant biomass, presents opportunities for organisms with a capacity for pathogenesis to become established in stressed soils.
Collapse
Affiliation(s)
- Andrew L. Neal
- Department of Sustainable Agriculture Science, Rothamsted Research, North Wyke, Devon, United Kingdom
| | - David Hughes
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Ian M. Clark
- Department of Sustainable Agriculture Science, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Penny R. Hirsch
- Department of Sustainable Agriculture Science, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| |
Collapse
|
16
|
Weitz KK, Smith ML, Hixson KK, Hill EA, Jansson JK, Hofmockel KS, Lipton MS. Real-Time Mass Spectrometry Measurements of Respiration Rates in Biological Systems. J Am Soc Mass Spectrom 2021; 32:648-652. [PMID: 33258588 DOI: 10.1021/jasms.0c00251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many organisms process carbon and other nutrients to generate energy through aerobic respiration where organic carbon compounds are broken down and oxygen is consumed, producing carbon dioxide and water. Respiration is indicative of active metabolism, and respiration rates are proportional to the amount of living biomass in an ecosystem. Although there are many methods for measuring respiration rates in the laboratory, current systems, such as infrared gas analyzers, are limited in their ability to independently resolve isotopomer fluxes across a range of relevant gases including both CO2 and O2 in real-time. Therefore, monitoring of biological respiration in real time under controlled laboratory conditions would enable better understanding of cellular physiology. To address this challenge, we developed a real time mass spectrometry (RTMS) manifold that simultaneously measures production and consumption of multiple gases and their isotopologues in seconds with the speed and sensitivity necessary to characterize rapidly changing respiration events as they occur. This universal manifold can be fitted to a variety of instruments and affords the same analytical precision and accuracy of the instrument while allowing for the real time measurements. Here, we paired the manifold to a single quad MS with an electron impact (EI) source operated in scan mode to detect extracted target gases by their respective masses (e.g., 12CO2 at mass 44, 13CO2 at 45). We demonstrated applicability of the RTMS instrument to different biological ecosystems (bacterial cultures, plants, and soil), and in all cases, we were able to detect simultaneous and rapid measurements of multiple gases in real time, providing novel insights into complex respiratory metabolism and the influence of biological and environmental factors.
Collapse
Affiliation(s)
- Karl K Weitz
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Montana L Smith
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kim K Hixson
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric A Hill
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Janet K Jansson
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kirsten S Hofmockel
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mary S Lipton
- Environmental and Biological Sciences Division Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
17
|
Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Corrigendum: Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci 2021; 7:619718. [PMID: 33732731 PMCID: PMC7959737 DOI: 10.3389/fmolb.2020.619718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
18
|
Jurelevicius D, Cotta SR, Montezzi LF, Dias ACF, Mason OU, Picão RC, Jansson JK, Seldin L. Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity. Environ Pollut 2021; 268:115757. [PMID: 33168375 DOI: 10.1016/j.envpol.2020.115757] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic activities in coastal marine ecosystems can lead to an increase in the abundance of potentially harmful microorganisms in the marine environment. To understand anthropogenic impacts on the marine microbiome, we first used publicly available microbial phylogenetic and functional data to establish a dataset of bacterial genera potentially related to pathogens that cause diseases (BGPRD) in marine organisms. Representatives of low-, medium- and highly impacted marine coastal environments were selected, and the abundance and composition of their microbial communities were determined by quantitative PCR and 16 S rRNA gene sequencing. In total, 72 BGPRD were cataloged, and 11, 36 and 37 BGPRD were found in low-, medium- and highly human-impacted ecosystems, respectively. The absolute abundance of BGPRD and the co-occurrence of antibiotic resistance genes (AGR) increased with the degree of anthropogenic perturbation in these ecosystems. Anthropogenically impacted coastal microbiomes were compositionally and functionally distinct from those of less impacted sites, presenting features that may contribute to adverse outcomes for marine macrobiota in the Anthropocene era.
Collapse
Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Simone R Cotta
- ESALQ - Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brazil
| | - Lara F Montezzi
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Armando C F Dias
- ESALQ - Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brazil
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Renata C Picão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Janet K Jansson
- Earth and Biological, Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
19
|
Suskind DL, Lee D, Kim YM, Wahbeh G, Singh N, Braly K, Nuding M, Nicora CD, Purvine SO, Lipton MS, Jansson JK, Nelson WC. The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn's Disease: A Randomized Diet Controlled Trial. Nutrients 2020; 12:nu12123749. [PMID: 33291229 PMCID: PMC7762109 DOI: 10.3390/nu12123749] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Crohn’s disease (CD) is a chronic inflammatory intestinal disorder associated with intestinal dysbiosis. Diet modulates the intestinal microbiome and therefore has a therapeutic potential. The aim of this study is to determine the potential efficacy of three versions of the specific carbohydrate diet (SCD) in active Crohn’s Disease. Methods: 18 patients with mild/moderate CD (PCDAI 15–45) aged 7 to 18 years were enrolled. Patients were randomized to either SCD, modified SCD(MSCD) or whole foods (WF) diet. Patients were evaluated at baseline, 2, 4, 8 and 12 weeks. PCDAI, inflammatory labs and multi-omics evaluations were assessed. Results: Mean age was 14.3 ± 2.9 years. At week 12, all participants (n = 10) who completed the study achieved clinical remission. The C-reactive protein decreased from 1.3 ± 0.7 at enrollment to 0.9 ± 0.5 at 12 weeks in the SCD group. In the MSCD group, the CRP decreased from 1.6 ± 1.1 at enrollment to 0.7 ± 0.1 at 12 weeks. In the WF group, the CRP decreased from 3.9 ± 4.3 at enrollment to 1.6 ± 1.3 at 12 weeks. In addition, the microbiome composition shifted in all patients across the study period. While the nature of the changes was largely patient specific, the predicted metabolic mode of the organisms increasing and decreasing in activity was consistent across patients. Conclusions: This study emphasizes the impact of diet in CD. Each diet had a positive effect on symptoms and inflammatory burden; the more exclusionary diets were associated with a better resolution of inflammation.
Collapse
Affiliation(s)
- David L. Suskind
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
- Correspondence: ; Tel.: +1-206-987-2521; Fax: +1-206-987-2721
| | - Dale Lee
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| | - Ghassan Wahbeh
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Namita Singh
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Kimberly Braly
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Mason Nuding
- Department of Pediatrics, Division of Gastroenterology, Seattle Children’s Hospital and University of Washington, Seattle, WA 98105, USA; (D.L.); (G.W.); (N.S.); (K.B.); (M.N.)
| | - Carrie D. Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (S.O.P.); (M.S.L.)
| | - Mary S. Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (S.O.P.); (M.S.L.)
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| | - William C. Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-M.K.); (C.D.N.); (J.K.J.); (W.C.N.)
| |
Collapse
|
20
|
Bradley R, Langley BO, Ryan JJ, Phipps J, Hanes DA, Stack E, Jansson JK, Metz TO, Stevens JF. Correction to: Xanthohumol microbiome and signature in healthy adults (the XMaS trial): a phase I triple-masked, placebo-controlled clinical trial. Trials 2020; 21:885. [PMID: 33106168 PMCID: PMC7586645 DOI: 10.1186/s13063-020-04834-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
21
|
Zegeye EK, Sadler NC, Lomas GX, Attah IK, Jansson JK, Hofmockel KS, Anderton CR, Wright AT. Activity-Based Protein Profiling of Chitin Catabolism. Chembiochem 2020; 22:717-723. [PMID: 33049124 DOI: 10.1002/cbic.202000616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/12/2020] [Indexed: 01/09/2023]
Abstract
The microbial catabolism of chitin, an abundant and ubiquitous environmental organic polymer, is a fundamental cog in terrestrial and aquatic carbon and nitrogen cycles. Despite the importance of this critical bio-geochemical function, there is a limited understanding of the synergy between the various hydrolytic and accessory enzymes involved in chitin catabolism. To address this deficit, we synthesized activity-based probes (ABPs) designed to target active chitinolytic enzymes by modifying the chitin subunits N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. We demonstrate the utility of these ABPs in determining the synergy between various enzymes involved in chitin catabolism. The strategy can be used to gain molecular-level insights that can be used to better understand microbial roles in soil bio-geochemical cycling in the face of a changing climate.
Collapse
Affiliation(s)
- Elias K Zegeye
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Gerard X Lomas
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Isaac K Attah
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
- Department of Ecology, Evolution and Organismal Biology Iowa State University, 251 Bessey Hall, Ames, Iowa (USA) 50011
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Aaron T Wright
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| |
Collapse
|
22
|
Bradley R, Langley BO, Ryan JJ, Phipps J, Hanes DA, Stack E, Jansson JK, Metz TO, Stevens JF. Xanthohumol microbiome and signature in healthy adults (the XMaS trial): a phase I triple-masked, placebo-controlled clinical trial. Trials 2020; 21:835. [PMID: 33028396 PMCID: PMC7542976 DOI: 10.1186/s13063-020-04769-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Natural products may provide a source for the discovery and development of adjunctive pharmacological interventions to modulate the inflammatory pathways contributing to chronic disease. Xanthohumol, a flavonoid from the hops plant (Humulus lupulus), has antioxidant and anti-inflammatory properties and may act as a prebiotic to the intestinal microbiota. Xanthohumol is not currently approved as a drug by the US Food and Drug Administration (FDA), but is available as a dietary supplement and ingredient in medical foods. To formally test the safety of xanthohumol, a phase I clinical trial ("XMaS") was designed and approved under an Investigational New Drug application to the US FDA. The main objective is to examine the clinical safety and subjective tolerability of xanthohumol in healthy adults compared to placebo. Additional aims are to monitor biomarkers related to inflammation, gut permeability, bile acid metabolism, routes, and in vivo products of xanthohumol metabolism, and to evaluate xanthohumol's impact on gut microbial composition. METHODS The safety and tolerability of xanthohumol in healthy adults will be evaluated in a triple-masked, randomized, placebo-controlled trial. Participants will be randomized to either 24 mg/day of xanthohumol or placebo for 8 weeks. Blood cell counts, hepatic and renal function tests, electrolytes, and self-reported health-related quality of life measures will be collected every 2 weeks. Participants will be queried for adverse events throughout the trial. Xanthohumol metabolites in blood, urine, and stool will be measured. Biomarkers to be evaluated include plasma tumor necrosis factor-alpha, various interleukins, soluble CD14, lipopolysaccharide-binding protein, fecal calprotectin, and bile acids to assess impact on inflammatory and gut permeability-related mechanisms in vivo. Stool samples will be analyzed to determine effects on the gut microbiome. DISCUSSION This phase I clinical trial of xanthohumol will assess safety and tolerability in healthy adults, collect extensive biomarker data for assessment of potential mechanism(s), and provide comparison data necessary for future phase II trials in chronic disease(s). The design and robustness of the planned safety and mechanistic evaluations planned provide a model for drug discovery pursuits from natural products. TRIAL REGISTRATION ClinicalTrials.gov NCT03735420 . Registered on November 8, 2018.
Collapse
Affiliation(s)
- Ryan Bradley
- National University of Natural Medicine, Portland, USA.
| | | | | | - John Phipps
- National University of Natural Medicine, Portland, USA
| | | | - Emily Stack
- National University of Natural Medicine, Portland, USA
| | | | - Thomas O Metz
- Pacific Northwest National Laboratory, Richland, USA
| | | |
Collapse
|
23
|
McClure R, Naylor D, Farris Y, Davison M, Fansler SJ, Hofmockel KS, Jansson JK. Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome. Front Microbiol 2020; 11:1987. [PMID: 32983014 PMCID: PMC7479069 DOI: 10.3389/fmicb.2020.01987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. Despite its importance, analysis of the soil microbiome is difficult due to its sheer complexity, with thousands of interacting species. Here, we reduced this complexity by developing model soil microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in soil that often requires the coordinated action of several microorganisms for complete metabolic degradation. Several soil consortia were derived that had tractable richness (30–50 OTUs) with diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. The resulting consortia could be stored as glycerol or lyophilized stocks at −80°C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. One of the consortia that was particularly stable was chosen as a model soil consortium (MSC-1) for further analysis. MSC-1 species interactions were studied using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Mycobacterium, Rhodococcus, and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. The knowledge gained from querying these communities and their interactions will enable better understanding of the soil microbiome and the roles these interactions play in this environment.
Collapse
Affiliation(s)
- Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dan Naylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michelle Davison
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
24
|
Kabwe MH, Vikram S, Mulaudzi K, Jansson JK, Makhalanyane TP. The gut mycobiota of rural and urban individuals is shaped by geography. BMC Microbiol 2020; 20:257. [PMID: 32807105 PMCID: PMC7430031 DOI: 10.1186/s12866-020-01907-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Understanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota. RESULTS Our participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers. CONCLUSIONS Together, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.
Collapse
Affiliation(s)
- Mubanga Hellen Kabwe
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Khodani Mulaudzi
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, Washington, 99352, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynwood Road, Hatfield, Pretoria, 0028, South Africa.
| |
Collapse
|
25
|
Ma B, Wang Y, Ye S, Liu S, Stirling E, Gilbert JA, Faust K, Knight R, Jansson JK, Cardona C, Röttjers L, Xu J. Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. Microbiome 2020; 8:82. [PMID: 32498714 PMCID: PMC7273686 DOI: 10.1186/s40168-020-00857-2] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/07/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. RESULTS This non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Video abstract CONCLUSION: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.
Collapse
Affiliation(s)
- Bin Ma
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Yiling Wang
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
| | - Shudi Ye
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
| | - Shan Liu
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
| | - Erinne Stirling
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, and BioEngineering, University of California San Diego, La Jolla, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, 99352, WA, USA
| | - Cesar Cardona
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, 60637, IL, USA
| | - Lisa Röttjers
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Jianming Xu
- College of Environmental and Resource Sciences, Zhejiang University, Institute of Soil and Water Resources and Environmental Science, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| |
Collapse
|
26
|
Lee JY, Sadler NC, Egbert RG, Anderton CR, Hofmockel KS, Jansson JK, Song HS. Deep learning predicts microbial interactions from self-organized spatiotemporal patterns. Comput Struct Biotechnol J 2020; 18:1259-1269. [PMID: 32612750 PMCID: PMC7298420 DOI: 10.1016/j.csbj.2020.05.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of two interacting organisms under diverse growth and interaction scenarios, the data of which was subsequently used to train deep neural networks. For small-size domains (100 µm × 100 µm) over which interaction coefficients are assumed to be invariant, we obtained fairly accurate predictions, as indicated by an average R2 value of 0.84. In application to relatively larger domains (450 µm × 450 µm) where interaction coefficients are varying in space, deep learning models correctly predicted spatial distributions of interaction coefficients without any additional training. Lastly, we evaluated our model against real biological data obtained using Pseudomonas fluorescens and Escherichia coli co-cultures treated with polymeric chitin or N-acetylglucosamine, the hydrolysis product of chitin. While P. fluorescens can utilize both substrates for growth, E. coli lacked the ability to degrade chitin. Consistent with our expectations, our model predicted context-dependent interactions across two substrates, i.e., degrader-cheater relationship on chitin polymers and competition on monomers. The combined use of the agent-based model and machine learning algorithm successfully demonstrates how to infer microbial interactions from spatially distributed data, presenting itself as a useful tool for the analysis of more complex microbial community interactions.
Collapse
Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Natalie C. Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G. Egbert
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S. Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hyun-Seob Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| |
Collapse
|
27
|
Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Correction to: Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:73. [PMID: 32466793 PMCID: PMC7257159 DOI: 10.1186/s40168-020-00870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
Collapse
Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Marine College, Shandong University, Weihai, 264209, China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - B Y Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David W Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| |
Collapse
|
28
|
Mao JH, Kim YM, Zhou YX, Hu D, Zhong C, Chang H, Brislawn CJ, Fansler S, Langley S, Wang Y, Peisl BYL, Celniker SE, Threadgill DW, Wilmes P, Orr G, Metz TO, Jansson JK, Snijders AM. Genetic and metabolic links between the murine microbiome and memory. Microbiome 2020; 8:53. [PMID: 32299497 PMCID: PMC7164142 DOI: 10.1186/s40168-020-00817-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/02/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Recent evidence has linked the gut microbiome to host behavior via the gut-brain axis [1-3]; however, the underlying mechanisms remain unexplored. Here, we determined the links between host genetics, the gut microbiome and memory using the genetically defined Collaborative Cross (CC) mouse cohort, complemented with microbiome and metabolomic analyses in conventional and germ-free (GF) mice. RESULTS A genome-wide association analysis (GWAS) identified 715 of 76,080 single-nucleotide polymorphisms (SNPs) that were significantly associated with short-term memory using the passive avoidance model. The identified SNPs were enriched in genes known to be involved in learning and memory functions. By 16S rRNA gene sequencing of the gut microbial community in the same CC cohort, we identified specific microorganisms that were significantly correlated with longer latencies in our retention test, including a positive correlation with Lactobacillus. Inoculation of GF mice with individual species of Lactobacillus (L. reuteri F275, L. plantarum BDGP2 or L. brevis BDGP6) resulted in significantly improved memory compared to uninoculated or E. coli DH10B inoculated controls. Untargeted metabolomics analysis revealed significantly higher levels of several metabolites, including lactate, in the stools of Lactobacillus-colonized mice, when compared to GF control mice. Moreover, we demonstrate that dietary lactate treatment alone boosted memory in conventional mice. Mechanistically, we show that both inoculation with Lactobacillus or lactate treatment significantly increased the levels of the neurotransmitter, gamma-aminobutyric acid (GABA), in the hippocampus of the mice. CONCLUSION Together, this study provides new evidence for a link between Lactobacillus and memory and our results open possible new avenues for treating memory impairment disorders using specific gut microbial inoculants and/or metabolites. Video Abstract.
Collapse
Affiliation(s)
- Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Marine College, Shandong University, Weihai, 264209 China
| | - Dehong Hu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Colin J. Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sarah Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Sasha Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033 Shandong China
| | - B. Y. Loulou Peisl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - David W. Threadgill
- Department of Veterinary Pathobiology, A&M University, College Station, Texas, USA
- Department of Molecular and Cellular Medicine Texas, A&M University, College Station, Texas, USA
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7, Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Galya Orr
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Thomas O. Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| |
Collapse
|
29
|
Prescott SL, Hancock T, Bland J, van den Bosch M, Jansson JK, Johnson CC, Kondo M, Katz D, Kort R, Kozyrskyj A, Logan AC, Lowry CA, Nanan R, Poland B, Robinson J, Schroeck N, Sinkkonen A, Springmann M, Wright RO, Wegienka G. Eighth Annual Conference of inVIVO Planetary Health: From Challenges to Opportunities. Int J Environ Res Public Health 2019; 16:ijerph16214302. [PMID: 31694316 PMCID: PMC6861902 DOI: 10.3390/ijerph16214302] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 11/19/2022]
Abstract
inVIVO Planetary Health (inVIVO) is a progressive scientific movement providing evidence, advocacy, and inspiration to align the interests and vitality of people, place, and planet. Our goal is to transform personal and planetary health through awareness, attitudes, and actions, and a deeper understanding of how all systems are interconnected and interdependent. Here, we present the abstracts and proceedings of our 8th annual conference, held in Detroit, Michigan in May 2019, themed “From Challenges, to Opportunities”. Our far-ranging discussions addressed the complex interdependent ecological challenges of advancing global urbanization, including the biopsychosocial interactions in our living environment on physical, mental, and spiritual wellbeing, together with the wider community and societal factors that govern these. We had a strong solutions focus, with diverse strategies spanning from urban-greening and renewal, nature-relatedness, nutritional ecology, planetary diets, and microbiome rewilding, through to initiatives for promoting resilience, positive emotional assets, traditional cultural narratives, creativity, art projects for personal and community health, and exploring ways of positively shifting mindsets and value systems. Our cross-sectoral agenda underscored the importance and global impact of local initiatives everywhere by contributing to new normative values as part of a global interconnected grass-roots movement for planetary health.
Collapse
Affiliation(s)
- Susan L. Prescott
- The ORIGINS Project, Telethon Kids Institute, University of Western Australia, Perth Childrens Hospital, Nedlands, WA 6009, Australia
- inVIVO Planetary Health of the Worldwide Universities Network (WUN), West New York, NJ 10704, USA;
- Correspondence:
| | - Trevor Hancock
- School of Public Health and Social Policy (retired), University of Victoria, Victoria, BC V8W 2Y2, Canada;
| | - Jeffrey Bland
- Personalized Lifestyle Medicine Institute, Tacoma, WA 98443, USA;
| | - Matilda van den Bosch
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Janet K. Jansson
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA 99352, USA;
| | - Christine C. Johnson
- Henry Ford Health System and Center for Urban Responses to Environmental Stressors (CURES), Wayne State University Detroit, MI 48202, USA; (C.C.J.); (G.W.)
| | - Michelle Kondo
- USDA Forest Service, Northern Research Station, Philadelphia, PA 19103, USA;
| | - David Katz
- Yale-Griffin Prevention Research Center, Yale University, Derby, CT 06418, USA;
| | - Remco Kort
- Department of Molecular Cell Biology, VU University Amsterdam (VUA), 1081 HV Amsterdam, The Netherlands;
| | - Anita Kozyrskyj
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Alan C. Logan
- inVIVO Planetary Health of the Worldwide Universities Network (WUN), West New York, NJ 10704, USA;
| | - Christopher A. Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA;
| | - Ralph Nanan
- Charles Perkins Centre Nepean, University of Sydney, Camperdown, NSW 2006, Australia;
| | - Blake Poland
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T, Canada;
| | - Jake Robinson
- Department of Landscape, University of Sheffield, Sheffield S10 2TN, UK;
| | | | - Aki Sinkkonen
- Ecosystems and Environment Research Program, University of Helsinki, 15140 Lahti, Finland;
| | - Marco Springmann
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK;
| | - Robert O. Wright
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Ganesa Wegienka
- Henry Ford Health System and Center for Urban Responses to Environmental Stressors (CURES), Wayne State University Detroit, MI 48202, USA; (C.C.J.); (G.W.)
| |
Collapse
|
30
|
Wang P, Wang Y, Langley SA, Zhou YX, Jen KY, Sun Q, Brislawn C, Rojas CM, Wahl KL, Wang T, Fan X, Jansson JK, Celniker SE, Zou X, Threadgill DW, Snijders AM, Mao JH. Diverse tumour susceptibility in Collaborative Cross mice: identification of a new mouse model for human gastric tumourigenesis. Gut 2019; 68:1942-1952. [PMID: 30842212 PMCID: PMC6839736 DOI: 10.1136/gutjnl-2018-316691] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The Collaborative Cross (CC) is a mouse population model with diverse and reproducible genetic backgrounds used to identify novel disease models and genes that contribute to human disease. Since spontaneous tumour susceptibility in CC mice remains unexplored, we assessed tumour incidence and spectrum. DESIGN We monitored 293 mice from 18 CC strains for tumour development. Genetic association analysis and RNA sequencing were used to identify susceptibility loci and candidate genes. We analysed genomes of patients with gastric cancer to evaluate the relevance of genes identified in the CC mouse model and measured the expression levels of ISG15 by immunohistochemical staining using a gastric adenocarcinoma tissue microarray. Association of gene expression with overall survival (OS) was assessed by Kaplan-Meier analysis. RESULTS CC mice displayed a wide range in the incidence and types of spontaneous tumours. More than 40% of CC036 mice developed gastric tumours within 1 year. Genetic association analysis identified Nfκb1 as a candidate susceptibility gene, while RNA sequencing analysis of non-tumour gastric tissues from CC036 mice showed significantly higher expression of inflammatory response genes. In human gastric cancers, the majority of human orthologues of the 166 mouse genes were preferentially altered by amplification or deletion and were significantly associated with OS. Higher expression of the CC036 inflammatory response gene signature is associated with poor OS. Finally, ISG15 protein is elevated in gastric adenocarcinomas and correlated with shortened patient OS. CONCLUSIONS CC strains exhibit tremendous variation in tumour susceptibility, and we present CC036 as a spontaneous laboratory mouse model for studying human gastric tumourigenesis.
Collapse
Affiliation(s)
- Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,Clinical Laboratory, Second Hospital of Shandong University, Jinan, China
| | - Sasha A Langley
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan-Xia Zhou
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA,College of Marine Science, Shandong University, Weihai, China
| | - Kuang-Yu Jen
- Department of Pathology, University of California Davis Medical Center, Sacramento, California, USA
| | - Qi Sun
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Colin Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carolina M Rojas
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Kimberly L Wahl
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Ting Wang
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiangshan Fan
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Xiaoping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - David W Threadgill
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, Texas, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
31
|
Kim YM, Snijders AM, Brislawn CJ, Stratton KG, Zink EM, Fansler SJ, Metz TO, Mao JH, Jansson JK. Light-Stress Influences the Composition of the Murine Gut Microbiome, Memory Function, and Plasma Metabolome. Front Mol Biosci 2019; 6:108. [PMID: 31681796 PMCID: PMC6813214 DOI: 10.3389/fmolb.2019.00108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome plays an important role in the mammalian host and when in proper balance helps protect health and prevent disease. Host environmental stress and its influence on the gut microbiome, health, and disease is an emerging area of research. Exposures to unnatural light cycles are becoming increasingly common due to travel and shift work. However, much remains unknown about how these changes influence the microbiome and host health. This information is needed to understand and predict the relationship between the microbiome and host response to altered sleep cycles. In the present study, we exposed three cohorts of mice to different light cycle regimens for 12 consecutive weeks; including continuous light, continuous dark, and a standard light dark regimen consisting of 12 h light followed by 12 h of dark. After exposure, motor and memory behavior, and the composition of the fecal microbiome and plasma metabolome were measured. Memory potential was significantly reduced in mice exposed to continuous light, whereas rotarod performance was minimally affected. The overall composition of the microbiome was relatively constant over time. However, Bacteroidales Rikenellaceae was relatively more abundant in mice exposed to continuous dark, while Bacteroidales S24-7 was relatively more abundant in mice exposed to continuous light. The plasma metabolome after the continuous dark exposure differed from the other exposure conditions. Several plasma metabolites, including glycolic acid, tryptophan, pyruvate, and several unidentified metabolites, were correlated to continuous dark and light exposure conditions. Networking analyses showed that serotonin was positively correlated with three microbial families (Rikenellaceae, Ruminococcaceae, and Turicibacteraceae), while tryptophan was negatively correlated with abundance of Bacteroidales S24-7 based on light exposure. This study provides the foundation for future studies into the mechanisms underlying the role of the gut microbiome on the murine host during light-dark stress.
Collapse
Affiliation(s)
- Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Colin J Brislawn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kelly G Stratton
- Computing and Analytics Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
32
|
Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists' warning to humanity: microorganisms and climate change. Nat Rev Microbiol 2019; 17:569-586. [PMID: 31213707 PMCID: PMC7136171 DOI: 10.1038/s41579-019-0222-5] [Citation(s) in RCA: 623] [Impact Index Per Article: 124.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 11/27/2022]
Abstract
In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.
Collapse
Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Baylis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Antje Boetius
- Alfred Wegener Institute, Helmholtz Center for Marine and Polar Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Aimée T Classen
- Rubenstein School of Environment and Natural Resources, and The Gund Institute for Environment, University of Vermont, Burlington, VT, USA
| | | | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Christine M Foreman
- Center for Biofilm Engineering, and Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - David A Hutchins
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science & Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - David S Reay
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Virginia I Rich
- Microbiology Department, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Department of Microbiology, and Department of Civil, Environmental and Geodetic Engineering, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Scott C Weaver
- Department of Microbiology and Immunology, and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
33
|
Jansson JK, Hofmockel KS. Corrigendum to “The soil microbiome — from metagenomics to metaphenomics” [Curr Opin Micrbiol 43 (June 2018) 162-168]. Curr Opin Microbiol 2019; 49:104. [DOI: 10.1016/j.mib.2019.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
34
|
Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell 2019; 177:1600-1618.e17. [PMID: 31150625 PMCID: PMC6993574 DOI: 10.1016/j.cell.2019.05.004] [Citation(s) in RCA: 562] [Impact Index Per Article: 112.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/11/2019] [Accepted: 04/30/2019] [Indexed: 01/02/2023]
Abstract
Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD or TD controls into germ-free mice and reveal that colonization with ASD microbiota is sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and modulates neuronal excitability in the brain. We propose that the gut microbiota regulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.
Collapse
Affiliation(s)
- Gil Sharon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Nikki Jamie Cruz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dae-Wook Kang
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Michael J Gandal
- Center for Autism Research and Treatment, Program in Neurobehavioral Genetics, Semel Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bo Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Erika M Zink
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Cameron P Casey
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Bryn C Taylor
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christianne J Lane
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Nancy G Isern
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - David W Hoyt
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J Sweredoski
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Annie Moradian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Biongineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Thomas O Metz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Program in Neurobehavioral Genetics, Semel Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, Semel Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ 85287, USA; Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| |
Collapse
|
35
|
Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 2019; 569:655-662. [PMID: 31142855 PMCID: PMC6650278 DOI: 10.1038/s41586-019-1237-9] [Citation(s) in RCA: 1328] [Impact Index Per Article: 265.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/16/2019] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. Crohn’s disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study’s infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi’omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases. The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.
Collapse
Affiliation(s)
- Jason Lloyd-Price
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Cesar Arze
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Melanie Schirmer
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Tiffany W Poon
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nadim J Ajami
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kevin S Bonham
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Holly Courtney
- Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Thomas G Graeber
- Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA, USA
| | - A Brantley Hall
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen Lake
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carol J Landers
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Himel Mallick
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mahadev Prasad
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Gholamali Rahnavard
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jenny Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Los Angeles, CA, USA
| | - Dmitry Shungin
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Odontology, Umeå University, Umeå, Sweden
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Richard A White
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | | | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lee A Denson
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Lab, Richland, WA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | | | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joseph F Petrosino
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Harland S Winter
- Department of Pediatrics, MassGeneral Hospital for Children, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|
36
|
Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med 2019; 24:392-400. [PMID: 29634682 PMCID: PMC7043356 DOI: 10.1038/nm.4517] [Citation(s) in RCA: 1209] [Impact Index Per Article: 241.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 02/14/2018] [Indexed: 12/13/2022]
Abstract
Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review, we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.
Collapse
Affiliation(s)
- Jack A Gilbert
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, Illinois, USA.,Bioscience Division, Argonne National Laboratory, Lemont, Illinois, USA.,Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Martin J Blaser
- New York University Langone Medical Center, New York, New York, USA
| | - J Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA.,Department of Computer Science & Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
37
|
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science 2019; 364:446. [PMID: 31048484 DOI: 10.1126/science.aax7509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
38
|
Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends Analyt Chem 2019; 116:292-299. [PMID: 31798197 DOI: 10.1016/j.trac.2019.04.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.
Collapse
Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A &M University, College Station, TX
| | - James N Dodds
- Department of Chemistry, NC State University, Raleigh, NC
| | - Jeremy Ash
- Department of Chemistry, NC State University, Raleigh, NC
| | - Denis Fourches
- Department of Chemistry, NC State University, Raleigh, NC
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Jason P Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Erin S Baker
- Department of Chemistry, NC State University, Raleigh, NC
| |
Collapse
|
39
|
Blakeley-Ruiz JA, Erickson AR, Cantarel BL, Xiong W, Adams R, Jansson JK, Fraser CM, Hettich RL. Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn's remission patients despite temporal variations in microbial taxa, genomes, and proteomes. Microbiome 2019; 7:18. [PMID: 30744677 PMCID: PMC6371617 DOI: 10.1186/s40168-019-0631-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/17/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues. It has been difficult, however, to elucidate the overall functional characteristics of this relationship because the microbiota can vary substantially in composition for healthy humans and possibly even more in individuals with gut disease conditions such as Crohn's disease. Overall, this suggests that microbial membership composition may not be the best way to characterize a phenotype. Alternatively, it seems to be more informative to examine and characterize the functional composition of a gut microbiome. Towards that end, this study examines 25 metaproteomes measured in several Crohn's disease patients' post-resection surgery across the course of 1 year, in order to examine persistence of microbial taxa, genes, proteins, and metabolic functional distributions across time in individuals whose microbiome might be more variable due to the gut disease condition. RESULTS The measured metaproteomes were highly personalized, with all the temporally-related metaproteomes clustering most closely by individual. In general, the metaproteomes were remarkably distinct between individuals and to a lesser extent within individuals. This prompted a need to characterize the metaproteome at a higher functional level, which was achieved by annotating identified protein groups with KEGG orthologous groups to infer metabolic modules. At this level, similar and redundant metabolic functions across multiple phyla were observed across time and between individuals. Tracking through these various metabolic modules revealed a clear path from carbohydrate, lipid, and amino acid degradation to central metabolism and finally the production of fermentation products. CONCLUSIONS The human gut metaproteome can vary quite substantially across time and individuals. However, despite substantial intra-individual variation in the metaproteomes, there is a clear persistence of conserved metabolic functions across time and individuals. Additionally, the persistence of these core functions is redundant across multiple phyla but is not always observable in the same sample. Finally, the gut microbiome's metabolism is not driven by a set of discrete linear pathways but a web of interconnected reactions facilitated by a network of enzymes that connect multiple molecules across multiple pathways.
Collapse
Affiliation(s)
- J Alfredo Blakeley-Ruiz
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison R Erickson
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Current address: Harvard Medical School, Cell Biology, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Brandi L Cantarel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Current address: Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Current address: U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, 20740, USA
| | - Rachel Adams
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Lab, Richland, WA, 99352, USA
| | - Claire M Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Graduate School of Genome Science & Technology, University of Tennessee, Knoxville, TN, 37996, USA.
| |
Collapse
|
40
|
Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Toward unrestricted use of public genomic data. Science 2019; 363:350-352. [PMID: 30679363 DOI: 10.1126/science.aaw1280] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Publication interests should not limit access to public data
Collapse
|
41
|
Boiteau RM, Fansler SJ, Farris Y, Shaw JB, Koppenaal DW, Pasa-Tolic L, Jansson JK. Siderophore profiling of co-habitating soil bacteria by ultra-high resolution mass spectrometry. Metallomics 2019; 11:166-175. [DOI: 10.1039/c8mt00252e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calcareous soil microbes complete for scarce iron by synthesizing diverse suites of siderophores detectable by ultra-high resolution mass spectrometry.
Collapse
Affiliation(s)
- Rene M. Boiteau
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
- College of Earth, Ocean, Atmospheric Sciences
| | - Sarah J. Fansler
- Biological Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Yuliya Farris
- College of Earth, Ocean, Atmospheric Sciences
- Oregon State University
- Corvallis
- USA
| | - Jared B. Shaw
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - David W. Koppenaal
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory
- Pacific Northwest National Laboratory
- Richland
- USA
| | - Janet K. Jansson
- Biological Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
| |
Collapse
|
42
|
Whidbey C, Sadler NC, Nair RN, Volk RF, DeLeon AJ, Bramer LM, Fansler SJ, Hansen JR, Shukla AK, Jansson JK, Thrall BD, Wright AT. A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome. J Am Chem Soc 2018; 141:42-47. [PMID: 30541282 DOI: 10.1021/jacs.8b09668] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Commensal microorganisms in the mammalian gut play important roles in host health and physiology, but a central challenge remains in achieving a detailed mechanistic understanding of specific microbial contributions to host biochemistry. New function-based approaches are needed that analyze gut microbial function at the molecular level by coupling detection and measurements of in situ biochemical activity with identification of the responsible microbes and enzymes. We developed a platform employing β-glucuronidase selective activity-based probes to detect, isolate, and identify microbial subpopulations in the gut responsible for this xenobiotic metabolism. We find that metabolic activity of gut microbiota can be plastic and that between individuals and during perturbation, phylogenetically disparate populations can provide β-glucuronidase activity. Our work links biochemical activity with molecular-scale resolution without relying on genomic inference.
Collapse
Affiliation(s)
- Christopher Whidbey
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Natalie C Sadler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Reji N Nair
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Regan F Volk
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Adrian J DeLeon
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Lisa M Bramer
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Sarah J Fansler
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Joshua R Hansen
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Anil K Shukla
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Janet K Jansson
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Brian D Thrall
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Aaron T Wright
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering , Washington State University , Pullman , Washington 99163 , United States
| |
Collapse
|
43
|
Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
Collapse
Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| |
Collapse
|
44
|
Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. Front Microbiol 2018; 9:1775. [PMID: 30158906 PMCID: PMC6104126 DOI: 10.3389/fmicb.2018.01775] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022] Open
Abstract
The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.
Collapse
Affiliation(s)
- Rachel Mackelprang
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Alyssa M. Grube
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Ederson da C. Jesus
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Chao Liang
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Randall D. Jackson
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Stefanie Kapucija
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Bayan Parsa
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
45
|
Müller O, Bang-Andreasen T, White RA, Elberling B, Taş N, Kneafsey T, Jansson JK, Øvreås L. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environ Microbiol 2018; 20:4328-4342. [PMID: 29971895 DOI: 10.1111/1462-2920.14348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.
Collapse
Affiliation(s)
- Oliver Müller
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway
| | - Toke Bang-Andreasen
- Department of Environmental Science, Aarhus University, DK-4000, Roskilde, Denmark.,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Bo Elberling
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Neslihan Taş
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Janet K Jansson
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
| |
Collapse
|
46
|
Phoma S, Vikram S, Jansson JK, Ansorge IJ, Cowan DA, Van de Peer Y, Makhalanyane TP. Agulhas Current properties shape microbial community diversity and potential functionality. Sci Rep 2018; 8:10542. [PMID: 30002454 PMCID: PMC6043601 DOI: 10.1038/s41598-018-28939-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/28/2018] [Indexed: 11/21/2022] Open
Abstract
Understanding the impact of oceanographic features on marine microbial ecosystems remains a major ecological endeavour. Here we assess microbial diversity, community structure and functional capacity along the Agulhas Current system and the Subtropical Front in the South Indian Ocean (SIO). Samples collected from the epipelagic, oxygen minimum and bathypelagic zones were analysed by 16S rRNA gene amplicon and metagenomic sequencing. In contrast to previous studies, we found high taxonomic richness in surface and deep water samples, but generally low richness for OMZ communities. Beta-diversity analysis revealed significant dissimilarity between the three water depths. Most microbial communities were dominated by marine Gammaproteobacteria, with strikingly low levels of picocyanobacteria. Community composition was strongly influenced by specific environmental factors including depth, salinity, and the availability of both oxygen and light. Carbon, nitrogen and sulfur cycling capacity in the SIO was linked to several autotrophic and copiotrophic Alphaproteobacteria and Gammaproteobacteria. Taken together, our data suggest that the environmental conditions in the Agulhas Current system, particularly depth-related parameters, substantially influence microbial community structure. In addition, the capacity for biogeochemical cycling of nitrogen and sulfur is linked primarily to the dominant Gammaproteobacteria taxa, whereas ecologically rare taxa drive carbon cycling.
Collapse
Affiliation(s)
- Sandra Phoma
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, P.O. Box 999, Richland, WA, USA
| | - Isabelle J Ansorge
- Department of Oceanography and Marine Research Institute (Ma-Re), University of Cape Town, Rondebosch, 7701, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa
- VIB Centre for Plant Systems Biology, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2, University of Pretoria, Pretoria, 0028, South Africa.
| |
Collapse
|
47
|
Kimbrel JA, Ballor N, Wu YW, David MM, Hazen TC, Simmons BA, Singer SW, Jansson JK. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front Microbiol 2018; 9:1492. [PMID: 30042744 PMCID: PMC6048260 DOI: 10.3389/fmicb.2018.01492] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.
Collapse
Affiliation(s)
- Jeffrey A Kimbrel
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Ballor
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yu-Wei Wu
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maude M David
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Terry C Hazen
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake A Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W Singer
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
48
|
Bottos EM, Kennedy DW, Romero EB, Fansler SJ, Brown JM, Bramer LM, Chu RK, Tfaily MM, Jansson JK, Stegen JC. Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities. FEMS Microbiol Ecol 2018; 94:5037918. [DOI: 10.1093/femsec/fiy110] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/13/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eric M Bottos
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC, V2C 0C8, Canada
| | - David W Kennedy
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Elvira B Romero
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Sarah J Fansler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Joseph M Brown
- Computational Biology, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Lisa M Bramer
- National Security Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| | - James C Stegen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99352, USA
| |
Collapse
|
49
|
Nicora CD, Burnum-Johnson KE, Nakayasu ES, Casey CP, White RA, Roy Chowdhury T, Kyle JE, Kim YM, Smith RD, Metz TO, Jansson JK, Baker ES. The MPLEx Protocol for Multi-omic Analyses of Soil Samples. J Vis Exp 2018. [PMID: 29912205 DOI: 10.3791/57343] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mass spectrometry (MS)-based integrated metaproteomic, metabolomic, and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges, since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for the simultaneous extraction of metabolites, proteins, and lipids (MPLEx) from the same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be both simple and robust for many sample types, even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.
Collapse
Affiliation(s)
- Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory
| | | | | | - Cameron P Casey
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Richard A White
- Biological Sciences Division, Pacific Northwest National Laboratory
| | | | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory;
| | - Erin S Baker
- Biological Sciences Division, Pacific Northwest National Laboratory;
| |
Collapse
|
50
|
Noguti J, Chan AA, Bandera B, Brislawn CJ, Protic M, Sim MS, Jansson JK, Bilchik AJ, Lee DJ. Both the intratumoral immune and microbial microenvironment are linked to recurrence in human colon cancer: results from a prospective, multicenter nodal ultrastaging trial. Oncotarget 2018; 9:23564-23576. [PMID: 29805756 PMCID: PMC5955112 DOI: 10.18632/oncotarget.25276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/08/2018] [Indexed: 12/15/2022] Open
Abstract
Colon cancer (CC) is the third most common cancer diagnosed in the United States and the incidence has been rising among young adults. We and others have shown a relationship between the immune infiltrate and prognosis, with improved disease-free survival (DFS) being associated with a higher expression of CD8+ T cells. We hypothesized that a microbial signature might be associated with intratumoral immune cells as well as DFS. We found that the relative abundance of one Operational Taxonomic Unit (OTU), OTU_104, was significantly associated with recurrence even after applying false discovery correction (HR 1.21, CI 1.08 to 1.36). The final multivariable model showed that DFS was influenced by three parameters: N-stage, CD8+ labeling, as well as this OTU_104 belonging to the order Clostridiales. Not only were CD8+ labeling and OTU_104 significant contributors in the final DFS model, but they were also inversely correlated to each other (p=0.022). Interestingly, CD8+ was also significantly associated with the microbiota composition in the tumor: CD8+ T cells was inversely correlated with alpha diversity (p=0.027) and significantly associated with the beta diversity. This study is the first to demonstrate an association among the intratumoral microbiome, CD8+ T cells, and recurrence in CC. An increased relative abundance of a specific OTU_104 was inversely associated with CD8+ T cells and directly associated with CC recurrence. The link between this microbe, CD8+ T cells, and DFS has not been previously shown.
Collapse
Affiliation(s)
- Juliana Noguti
- Dirks/Dougherty Laboratory for Cancer Research, Department of Translational Immunology, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.,Los Angeles Biomedical Research Institute, Harbor - UCLA Medical Center, Torrance, CA, USA
| | - Alfred A Chan
- Dirks/Dougherty Laboratory for Cancer Research, Department of Translational Immunology, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.,Los Angeles Biomedical Research Institute, Harbor - UCLA Medical Center, Torrance, CA, USA
| | - Bradley Bandera
- Department of Surgical Oncology. The John Wayne Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mladjan Protic
- University of Novi Sad, Faculty of Medicine, Novi Sad, Serbia.,Oncology Institute of Vojvodina, Sremska Kamenica, Serbia
| | - Myung S Sim
- UCLA Department of Medicine, Statistics Core, Los Angeles, CA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Anton J Bilchik
- Department of Surgical Oncology. The John Wayne Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Delphine J Lee
- Dirks/Dougherty Laboratory for Cancer Research, Department of Translational Immunology, John Wayne Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA.,Los Angeles Biomedical Research Institute, Harbor - UCLA Medical Center, Torrance, CA, USA.,Division of Dermatology, Department of Medicine, Harbor - UCLA Medical Center, Torrance, CA, USA.,David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
| |
Collapse
|