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Article ; Online: Strong ethanol- and frequency-dependent ecological interactions in a community of wine-fermenting yeasts.

Lax, Simon / Gore, Jeff

Communications biology

2023 Volume 6, Issue 1, Page(s) 939

Abstract: Natural wine fermentation depends on a complex consortium of native microorganisms rather than inoculation of industrial yeast strains. While this diversity of yeasts can result in an increased repertoire of wine flavors and aromas, it can also result in ...

Abstract	Natural wine fermentation depends on a complex consortium of native microorganisms rather than inoculation of industrial yeast strains. While this diversity of yeasts can result in an increased repertoire of wine flavors and aromas, it can also result in the inhibition of Saccharomyces cerevisiae, which is uniquely able to complete fermentation. Understanding how yeast species interact with each other within the wine-fermenting community and disentangling ecological interactions from environmental impacts on growth rates, is key to developing synthetic communities that can provide the sensory benefits of natural fermentation while lowering the risk of stuck ferments. Here, we co-culture all pairwise combinations of five commonly isolated wine-fermenting yeasts and show that competitive outcomes are a strong function of ethanol concentration, with frequency-dependent bistable interactions common at low alcohol and an increasingly transitive competitive hierarchy developing as alcohol increases. We also show that pairwise outcomes are predictive of five-species community outcomes, and that frequency dependence in pairwise interactions propagates to alternative states in the full community, highlighting the importance of species abundance as well as composition. We also observe that monoculture growth rates are only weakly predictive of competitive success, highlighting the need to incorporate ecological interactions when designing synthetic fermenting communities.
MeSH term(s)	Ethanol ; Wine ; Saccharomyces cerevisiae ; Coculture Techniques ; Fermentation
Chemical Substances	Ethanol (3K9958V90M)
Language	English
Publishing date	2023-09-13
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05284-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Higher temperatures generically favour slower-growing bacterial species in multispecies communities.

Lax, Simon / Abreu, Clare I / Gore, Jeff

Nature ecology & evolution

2020 Volume 4, Issue 4, Page(s) 560–567

Abstract: Temperature is one of the fundamental environmental variables that determine the composition and function of microbial communities. However, a predictive understanding of how microbial communities respond to changes in temperature is lacking, partly ... ...

Abstract	Temperature is one of the fundamental environmental variables that determine the composition and function of microbial communities. However, a predictive understanding of how microbial communities respond to changes in temperature is lacking, partly because it is not obvious which aspects of microbial physiology determine whether a species could benefit from a change in the temperature. Here we incorporate how microbial growth rates change with temperature into a modified Lotka-Volterra competition model and predict that higher temperatures should-in general-favour the slower-growing species in a bacterial community. We experimentally confirm this prediction in pairwise cocultures assembled from a diverse set of species and show that these changes to pairwise outcomes with temperature are also predictive of changing outcomes in three-species communities, suggesting that our theory may be applicable to more-complex assemblages. Our results demonstrate that it is possible to predict how bacterial communities will shift with temperature knowing only the growth rates of the community members. These results provide a testable hypothesis for future studies of more-complex natural communities and we hope that this work will help to bridge the gap between ecological theory and the complex dynamics observed in metagenomic surveys.
MeSH term(s)	Bacteria ; Hot Temperature ; Microbiota ; Temperature
Language	English
Publishing date	2020-03-02
Publishing country	England
Document type	Journal Article
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-020-1126-5
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Article ; Online: Uncovering the role of Symbiodiniaceae assemblage composition and abundance in coral bleaching response by minimizing sampling and evolutionary biases.

Swain, Timothy D / Lax, Simon / Backman, Vadim / Marcelino, Luisa A

BMC microbiology

2020 Volume 20, Issue 1, Page(s) 124

Abstract: Background: Biodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae, which offer diverse functional capabilities to their hosts. The number of unique symbiotic ... ...

Abstract	Background: Biodiversity and productivity of coral-reef ecosystems depend upon reef-building corals and their associations with endosymbiotic Symbiodiniaceae, which offer diverse functional capabilities to their hosts. The number of unique symbiotic partners (richness) and relative abundances (evenness) have been hypothesized to affect host response to climate change induced thermal stress. Symbiodiniaceae assemblages with many unique phylotypes may provide greater physiological flexibility or form less stable symbioses; assemblages with low abundance phylotypes may allow corals to retain thermotolerant symbionts or represent associations with less-suitable symbionts. Results: Here we demonstrate that true richness of Symbiodiniaceae phylotype assemblages is generally not discoverable from direct enumeration of unique phylotypes in association records and that cross host-species comparisons are biased by sampling and evolutionary patterns among species. These biases can be minimized through rarefaction of richness (rarefied-richness) and evenness (Probability of Interspecific Encounter, PIE), and analyses that account for phylogenetic patterns. These standardized metrics were calculated for individual Symbiodiniaceae assemblages composed of 377 unique ITS2 phylotypes associated with 123 coral species. Rarefied-richness minimized correlations with sampling effort, while maintaining important underlying characteristics across host bathymetry and geography. Phylogenetic comparative methods reveal significant increases in coral bleaching and mortality associated with increasing Symbiodiniaceae assemblage richness and evenness at the level of host species. Conclusions: These results indicate that the potential flexibility afforded by assemblages characterized by many phylotypes present at similar relative abundances does not result in decreased bleaching risk and point to the need to characterize the overall functional and genetic diversity of Symbiodiniaceae assemblages to quantify their effect on host fitness under climate change.
MeSH term(s)	Alveolata/classification ; Alveolata/isolation & purification ; Animals ; Anthozoa/classification ; Anthozoa/parasitology ; Anthozoa/physiology ; Biodiversity ; Biological Evolution ; Coral Reefs ; Phylogeny ; Symbiosis ; Thermotolerance
Language	English
Publishing date	2020-05-19
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2041505-9
ISSN	1471-2180 ; 1471-2180
ISSN (online)	1471-2180
ISSN	1471-2180
DOI	10.1186/s12866-020-01765-z
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Article: A Phylogeny-Informed Analysis of the Global Coral-Symbiodiniaceae Interaction Network Reveals that Traits Correlated with Thermal Bleaching Are Specific to Symbiont Transmission Mode.

Swain, Timothy D / Lax, Simon / Gilbert, Jack / Backman, Vadim / Marcelino, Luisa A

mSystems

2021 Volume 6, Issue 3

Abstract: The complex network of associations between corals and their dinoflagellates (family Symbiodiniaceae) are the basis of coral reef ecosystems but are sensitive to increasing global temperatures. Coral-symbiont interactions are restricted by ecological and ...

Abstract	The complex network of associations between corals and their dinoflagellates (family Symbiodiniaceae) are the basis of coral reef ecosystems but are sensitive to increasing global temperatures. Coral-symbiont interactions are restricted by ecological and evolutionary determinants that constrain partner choice and influence holobiont response to environmental stress; however, little is known about how these processes shape thermal resilience of the holobiont. Here, we built a network of global coral-Symbiodiniaceae associations, mapped species traits (e.g., symbiont transmission mode and biogeography) and phylogenetic relationships of both partners onto the network, and assigned thermotolerance to both host and symbiont nodes. Using network analysis and phylogenetic comparative methods, we determined the contribution of species traits to thermal resilience of the holobiont, while accounting for evolutionary patterns among species. We found that the network shows nonrandom interactions among species, which are shaped by evolutionary history, symbiont transmission mode (horizontally transmitted [HT] or vertically transmitted [VT] corals) and biogeography. Coral phylogeny, but not Symbiodiniaceae phylogeny, symbiont transmission mode, or biogeography, was a good predictor of thermal resilience. Closely related corals have similar Symbiodiniaceae interaction patterns and bleaching susceptibilities. Nevertheless, the association patterns that explain increased host thermal resilience are not generalizable across the entire network but are instead unique to HT and VT corals. Under nonstress conditions, thermally resilient VT coral species associate with thermotolerant phylotypes and limit their number of unique symbionts and overall symbiont thermotolerance diversity, while thermally resilient HT coral species associate with a few host-specific symbiont phylotypes.
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00266-21
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Article ; Online: Hospital-associated microbiota and implications for nosocomial infections.

Lax, Simon / Gilbert, Jack A

Trends in molecular medicine

2015 Volume 21, Issue 7, Page(s) 427–432

Abstract: The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual ... ...

Abstract	The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.
MeSH term(s)	Cross Infection/epidemiology ; Environmental Microbiology ; Hospitals/statistics & numerical data ; Humans ; Microbiota/physiology
Language	English
Publishing date	2015-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2036490-8
ISSN	1471-499X ; 1471-4914
ISSN (online)	1471-499X
ISSN	1471-4914
DOI	10.1016/j.molmed.2015.03.005
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Article ; Online: Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures.

Richardson, Miles / Gottel, Neil / Gilbert, Jack A / Lax, Simon

mBio

2019 Volume 10, Issue 4

Abstract: The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating ...

Abstract	The microbiota of the built environment is an amalgamation of both human and environmental sources. While human sources have been examined within single-family households or in public environments, it is unclear what effect a large number of cohabitating people have on the microbial communities of their shared environment. We sampled the public and private spaces of a college dormitory, disentangling individual microbial signatures and their impact on the microbiota of common spaces. We compared multiple methods for marker gene sequence clustering and found that minimum entropy decomposition (MED) was best able to distinguish between the microbial signatures of different individuals and was able to uncover more discriminative taxa across all taxonomic groups. Further, weighted UniFrac- and random forest-based graph analyses uncovered two distinct spheres of hand- or shoe-associated samples. Using graph-based clustering, we identified spheres of interaction and found that connection between these clusters was enriched for hands, implicating them as a primary means of transmission. In contrast, shoe-associated samples were found to be freely interacting, with individual shoes more connected to each other than to the floors they interact with. Individual interactions were highly dynamic, with groups of samples originating from individuals clustering freely with samples from other individuals, while all floor and shoe samples consistently clustered together.
MeSH term(s)	Entropy ; Genetic Markers/genetics ; Humans ; Microbiota/physiology ; Phylogeny ; Students/statistics & numerical data
Chemical Substances	Genetic Markers
Language	English
Publishing date	2019-07-30
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.01054-19
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Article ; Online: Our interface with the built environment: immunity and the indoor microbiota.

Lax, Simon / Nagler, Cathryn R / Gilbert, Jack A

Trends in immunology

2015 Volume 36, Issue 3, Page(s) 121–123

Abstract: The rise of urbanization and an increasingly indoor lifestyle has affected human interactions with our microbiota in unprecedented ways. We discuss how this lifestyle may influence immune development and function, and argue that it is time that we ... ...

Abstract	The rise of urbanization and an increasingly indoor lifestyle has affected human interactions with our microbiota in unprecedented ways. We discuss how this lifestyle may influence immune development and function, and argue that it is time that we examined ways to manipulate the indoor environment to increase our exposure to a wider phylogeny of microorganisms. An important step is to continue to engage citizen scientists in the efforts to characterize our interactions with the diverse microbial environments that we inhabit.
MeSH term(s)	Ecological Systems, Closed ; Environment ; Environment Design/trends ; Humans ; Immunity ; Information Dissemination ; Metagenome/immunology ; Microbiota/immunology ; Social Media ; Symbiosis/immunology ; Urbanization/trends
Language	English
Publishing date	2015-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2036831-8
ISSN	1471-4981 ; 1471-4906
ISSN (online)	1471-4981
ISSN	1471-4906
DOI	10.1016/j.it.2015.01.001
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Zs.A 1601: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Detecting personal microbiota signatures at artificial crime scenes.

Hampton-Marcell, Jarrad T / Larsen, Peter / Anton, Tifani / Cralle, Lauren / Sangwan, Naseer / Lax, Simon / Gottel, Neil / Salas-Garcia, Mariana / Young, Candace / Duncan, George / Lopez, Jose V / Gilbert, Jack A

Forensic science international

2020 Volume 313, Page(s) 110351

Abstract: When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique ... ...

Abstract	When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique microbial sequence variants between human skin and building surfaces in three experimental conditions: over time during controlled and uncontrolled incidental interactions with a door handle, and during multiple mock burglaries in ten real residences. We demonstrate that humans (n = 30) leave behind microbial signatures that can be used to track interaction with various surfaces within a building, but the likelihood of accurately detecting the specific burglar for a given home was between 20-25%. Also, the human microbiome contains rare microbial taxa that can be combined to create a unique microbial profile, which when compared to 600 other individuals can improve our ability to link an individual 'burglar' to a residence. In total, 5512 discriminating, non-singleton unique exact sequence variants (uESVs) were identified as unique to an individual, with a minimum of 1 and a maximum of 568, suggesting some people maintain a greater degree of unique taxa compared to our population of 600. Approximate 60-77% of the unique exact sequence variants originated from the hands of participants, and these microbial discriminators spanned 36 phyla but were dominated by the Proteobacteria (34%). A fitted regression generated to determine whether an intruder's uESVs found on door handles in an office decayed over time in the presence or absence of office workers, found no significant shift in proportion of uESVs over time irrespective of the presence of office workers. While it was possible to detect the correct burglars' microbiota as having contributed to the invaded space, the predictions were very weak in comparison to accepted forensic standards. This suggests that at this time 16S rRNA amplicon sequencing of the built environment microbiota cannot be used as a reliable trace evidence standard for criminal investigations.
MeSH term(s)	Crime ; Forensic Sciences/methods ; Humans ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/microbiology ; Statistics as Topic ; Touch
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2020-05-30
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	424042-x
ISSN	1872-6283 ; 0379-0738
ISSN (online)	1872-6283
ISSN	0379-0738
DOI	10.1016/j.forsciint.2020.110351
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Article ; Online: Microbial and metabolic succession on common building materials under high humidity conditions.

Lax, Simon / Cardona, Cesar / Zhao, Dan / Winton, Valerie J / Goodney, Gabriel / Gao, Peng / Gottel, Neil / Hartmann, Erica M / Henry, Chris / Thomas, Paul M / Kelley, Scott T / Stephens, Brent / Gilbert, Jack A

Nature communications

2019 Volume 10, Issue 1, Page(s) 1767

Abstract: Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied ...

Abstract	Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.
MeSH term(s)	Bacteria/genetics ; Bacteria/isolation & purification ; Bacteria/metabolism ; Construction Materials/microbiology ; Environmental Monitoring/methods ; Fungi/genetics ; Fungi/isolation & purification ; Fungi/metabolism ; Humidity ; Phylogeny ; RNA, Ribosomal, 16S/isolation & purification ; Viruses/genetics ; Viruses/isolation & purification ; Viruses/metabolism
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2019-04-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-09764-z
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Article: Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.

Cardona, Cesar / Lax, Simon / Larsen, Peter / Stephens, Brent / Hampton-Marcell, Jarrad / Edwardson, Christian F / Henry, Chris / Van Bonn, Bill / Gilbert, Jack A

mSystems

2018 Volume 3, Issue 3

Abstract: Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and ... ...

Abstract	Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability.
Language	English
Publishing date	2018-05-29
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00052-18
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