Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

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Spatial heterogeneity of the shorebird gastrointestinal microbiome

Royal Society Open Science ◽

10.1098/rsos.191609 ◽

2020 ◽

Vol 7 (1) ◽

pp. 191609

Author(s):

Kirsten Grond ◽

Hannah Guilani ◽

Sarah M. Hird

Keyword(s):

Microbial Communities ◽

Large Intestine ◽

Alpha Diversity ◽

Source Tracking ◽

Similar Species ◽

Gastrointestinal Microbiome ◽

Semipalmated Sandpiper ◽

Microbial Ecosystems ◽

Genus Richness ◽

Intestine Microbiome

The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

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Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants

Applied and Environmental Microbiology ◽

10.1128/aem.00934-13 ◽

2013 ◽

Vol 79 (17) ◽

pp. 5214-5223 ◽

Cited By ~ 136

Author(s):

Nicholas A. Bokulich ◽

David A. Mills

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Microbial Consortia ◽

True Nature ◽

Specific Product ◽

Site Specific ◽

Content Type ◽

Microbial Ecosystems ◽

Spatial Diversification ◽

Regional Product

ABSTRACTCheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarilyDebaryomycesandLactococcus, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific “house” microbiota, which may play a role in shaping site-specific product characteristics.

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Microbial Potlatch: Cell-level adaptation of leakiness of metabolites leads to resilient symbiosis among diverse cells

10.1101/2020.11.06.370924 ◽

2020 ◽

Author(s):

Jumpei F Yamagishi ◽

Nen Saito ◽

Kunihiko Kaneko

Keyword(s):

Growth Rate ◽

Microbial Communities ◽

Cell Level ◽

Frequency Dependent ◽

Symbiotic Relationships ◽

Microbial Species ◽

Nutrient Limitations ◽

Environmental Perturbations ◽

Microbial Ecosystems ◽

Diverse Species

AbstractMicrobial communities display extreme diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. By noting that cells can enhance their own growth rate by leakage of essential metabolites, we show that such leaker cells can benefit from coexistence with cells that consume the leaked chemicals in the environment. This leads to an unusual form of mutualism between “leaker” and “consumer” cells, resulting in frequency-dependent coexistence of multiple microbial species, as supported by extensive simulations. Remarkably, such symbiotic relationships generally evolve when each species adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations, leading to ecosystems with diverse species exchanging many metabolites with each other. In addition, such ecosystems are resilient against structural and environmental perturbations. Thus, we present a new basis for diverse, complex microbial ecosystems.

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A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbiome ◽

10.1186/s40168-019-0754-y ◽

2019 ◽

Vol 7 (1) ◽

Cited By ~ 5

Author(s):

Daniel Aguirre de Cárcer

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Phylogenetic Signal ◽

A Priori ◽

Amplicon Sequencing ◽

Bioinformatic Analysis ◽

Microbial Ecosystems ◽

And Function ◽

Microbial Community Assembly

Abstract Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs’ identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

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Review and perspective on mathematical modeling of microbial ecosystems

Biochemical Society Transactions ◽

10.1042/bst20170265 ◽

2018 ◽

Vol 46 (2) ◽

pp. 403-412 ◽

Cited By ~ 22

Author(s):

Antonella Succurro ◽

Oliver Ebenhöh

Keyword(s):

Microbial Communities ◽

Multiple Scales ◽

Macroscopic Description ◽

Modeling Methods ◽

Societal Challenges ◽

Microbial Ecosystems ◽

Differential Equation Models ◽

Spatio Temporal ◽

Temporal Interactions ◽

Stoichiometric Models

Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial ‘who is there?’ question. An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.

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The Vulnerability of Microbial Ecosystems in A Changing Climate: Potential Impact in Shark Bay

Life ◽

10.3390/life9030071 ◽

2019 ◽

Vol 9 (3) ◽

pp. 71 ◽

Cited By ~ 3

Author(s):

Reinold ◽

Wong ◽

MacLeod ◽

Meltzer ◽

Thompson ◽

...

Keyword(s):

Climate Change ◽

Microbial Communities ◽

Microbial Mats ◽

Extreme Weather ◽

Extreme Weather Events ◽

Shark Bay ◽

Changing Climate ◽

Microbial Ecosystems ◽

Weather Events ◽

Potential Impact

The potential impact of climate change on eukaryotes, including humans, has been relatively well described. In contrast, the contribution and susceptibility of microorganisms to a changing climate have, until recently, received relatively less attention. In this review, the importance of microorganisms in the climate change discourse is highlighted. Microorganisms are responsible for approximately half of all primary production on earth, support all forms of macroscopic life whether directly or indirectly, and often persist in “extreme” environments where most other life are excluded. In short, microorganisms are the life support system of the biosphere and therefore must be included in decision making regarding climate change. Any effects climate change will have on microorganisms will inevitably impact higher eukaryotes and the activity of microbial communities in turn can contribute to or alleviate the severity of the changing climate. It is of vital importance that unique, fragile, microbial ecosystems are a focus of research efforts so that their resilience to extreme weather events and climate change are thoroughly understood and that conservation efforts can be implemented as a response. One such ecosystem under threat are the evolutionarily significant microbial mats and stromatolites, such as those present in Shark Bay, western Australia. Climate change models have suggested the duration and severity of extreme weather events in this region will increase, along with rising temperatures, sea levels, and ocean acidification. These changes could upset the delicate balance that fosters the development of microbial mats and stromatolites in Shark Bay. Thus, the challenges facing Shark Bay microbial communities will be presented here as a specific case study.

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Independent host- and bacterium-based determinants protect a model symbiosis from phage predation

10.1101/2021.07.09.451802 ◽

2021 ◽

Author(s):

Jonathan B Lynch ◽

Brittany D Bennett ◽

Bryan D Merrill ◽

Edward G Ruby ◽

Andrew J Hryckowian

Keyword(s):

Extracellular Matrix ◽

Microbial Communities ◽

Marine Bacterium ◽

Vibrio Fischeri ◽

Euprymna Scolopes ◽

Ambient Seawater ◽

Bacterial Populations ◽

Microbial Ecosystems ◽

Shed Light

Bacteriophages (phages) are diverse and abundant constituents of microbial communities worldwide, and are capable of modulating bacterial populations in diverse ways. Here we describe a novel phage, ϕHNL01, which infects the marine bacterium Vibrio fischeri. We use culture-based approaches to demonstrate that mutations in the exopolysaccharide locus of V. fischeri render this bacterium resistant to infection by ϕHNL01, highlighting the extracellular matrix as a key determinant of phage tropism in this interaction. Additionally, using the natural symbiosis between V. fischeri and the squid Euprymna scolopes, we show that during colonization, V. fischeri is protected from phage present in the ambient seawater. Taken together, these findings shed light on independent yet synergistic host- and bacterium-based strategies for resisting symbiosis-disrupting phage predation, and present important implications for understanding these strategies in the context of host-associated microbial ecosystems.

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Engineering Host Microbiome for Crop Improvement and Sustainable Agriculture

Frontiers in Microbiology ◽

10.3389/fmicb.2021.635917 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sanjana Kaul ◽

Malvi Choudhary ◽

Suruchi Gupta ◽

Manoj K. Dhar

Keyword(s):

Microbial Communities ◽

Crop Improvement ◽

Nutrient Recycling ◽

Stress Physiology ◽

Plant Fitness ◽

New Paradigm ◽

Symbiotic Interactions ◽

Microbial Ecosystems ◽

Resistant Genotypes ◽

Plant Microbiome

Dynamic consortium of microbial communities (bacteria, fungi, protists, viruses, and nematodes) colonizing multiple tissue types and coevolving conclusively with the host plant is designated as a plant microbiome. The interplay between plant and its microbial mutualists supports several agronomic functions, establishing its crucial role in plant beneficial activities. Deeper functional and mechanistic understanding of plant-microbial ecosystems will render many “ecosystem services” by emulating symbiotic interactions between plants, soil, and microbes for enhanced productivity and sustainability. Therefore, microbiome engineering represents an emerging biotechnological tool to directly add, remove, or modify properties of microbial communities for higher specificity and efficacy. The main goal of microbiome engineering is enhancement of plant functions such as biotic/abiotic stresses, plant fitness and productivities, etc. Various ecological-, biochemical-, and molecular-based approaches have come up as a new paradigm for disentangling many microbiome-based agromanagement hurdles. Furthermore, multidisciplinary approaches provide a predictive framework in achieving a reliable and sustainably engineered plant-microbiome for stress physiology, nutrient recycling, and high-yielding disease-resistant genotypes.

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Complexity-stability relationship in empirical microbial ecosystems

10.1101/2021.07.29.454345 ◽

2021 ◽

Author(s):

Yogev Yonatan ◽

Guy Amit ◽

Amir Bashan ◽

Yonatan Friedman

Keyword(s):

Microbial Communities ◽

A Priori ◽

Interaction Network ◽

Ecological Systems ◽

Resident Species ◽

Computational Framework ◽

Microbial Ecosystems ◽

The Rich ◽

Central Paradigm ◽

Geographical Locations

May's stability theory, which holds that large ecosystems can be stable up to a critical level of complexity, a product of the number of resident species and the intensity of their interactions, has been a central paradigm in theoretical ecology. So far, however, empirically demonstrating this theory in real ecological systems has been a long-standing challenge, with inconsistent results. Especially, it is unknown whether this theory is pertinent in the rich and complex communities of natural microbiomes, mainly due to the challenge of reliably reconstructing such large ecological interaction networks. Here, we introduce a novel computational framework for estimating an ecosystem's complexity without relying on a priori knowledge of its underlying interaction network. By applying this method to human-associated microbial communities from different body sites and sponge-associated microbial communities from different geographical locations, we found that in both cases the communities display a pronounced trade-off between the number of species and their effective connectance. These results suggest that natural microbiomes are shaped by stability constraints, which limit their complexity.

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