scholarly journals Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

2019 ◽  
Author(s):  
Aarthi Ravikrishnan ◽  
Lars M Blank ◽  
Smita Srivastava ◽  
Karthik Raman
Keyword(s):  
Pichia Stipitis ◽  
Microbial Consortia ◽  
Integrated Modelling ◽  
Maximum Benefit ◽  
Single Organism ◽  
Hplc Profiles ◽  
Metabolic Interactions ◽  
Experimental Approaches ◽  
Pathway Analyses ◽  
Micro Organisms

ABSTRACTMicrobial co-cultures have been used in several biotechnological applications. Within these co-cultures, the micro-organisms tend to interact with each other and perform complex actions vis-à-vis a single organism. Investigating metabolic interactions in microbial co-cultures is crucial in designing microbial consortia tailored for specific applications. In this study, we present a pipeline integrating modelling and experimental approaches to understand metabolic interactions between organisms in a community. We define a new index named Metabolic Support Index (MSI), which quantifies the benefits derived by each organism in the presence of the other when grown as a co-culture. We computed MSI for several experimentally demonstrated co-culture systems and showed that MSI, as a metric, accurately identifies the organism that derives the maximum benefit. We also computed MSI for a commonly used yeast co-culture consisting of Saccharomyces cerevisiae and Pichia stipitis and observed that the latter derives higher benefit from the interaction. Further, we designed two-stage experiments to study mutual interactions and showed that P. stipitis indeed derives the maximum benefit from the interaction, as shown from our computational predictions. Also, using our previously developed computational tool MetQuest, we identified all the metabolic exchanges happening between these organisms by analysing the pathways spanning the two organisms. By analysing the HPLC profiles and studying the isotope labelling, we show that P. stipitis consumes the ethanol produced by S. cerevisiae when grown on glucose-rich medium under aerobic conditions, as also indicated by our in silico pathway analyses. Our approach represents an important step in understanding metabolic interactions in microbial communities through an integrating framework of modelling and experiments.

scholarly journals Carbohydrate complexity structures stable diversity in gut-derived microbial consortia under high dilution pressure

2020 ◽  
Author(s):  
Tianming Yao ◽  
Ming-Hsu Chen ◽  
Stephen R. Lindemann
Keyword(s):  
Microbial Diversity ◽  
Structural Complexity ◽  
Structure And Function ◽  
Microbial Consortia ◽  
Carbohydrate Structure ◽  
High Dilution ◽  
Chemical Complexity ◽  
Metabolic Interactions ◽  
And Function

ABSTRACTDietary fibers are major substrates for the colonic microbiota, but the structural specificity of these fibers for the diversity, structure, and function of gut microbial communities are poorly understood. Here, we employed an in vitro sequential batch fecal culture approach to determine: 1) whether the chemical complexity of a carbohydrate structure influences its ability to maintain microbial diversity in the face of high dilution pressure and 2) whether substrate structuring or obligate microbe-microbe metabolic interactions (e.g. exchange of amino acids or vitamins) exert more influence on maintained diversity. Sorghum arabinoxylan (SAX, complex polysaccharide), inulin (low-complexity oligosaccharide) and their corresponding monosaccharide controls were selected as model carbohydrates. Our results demonstrate that complex carbohydrates stably sustain diverse microbial consortia. Further, very similar final consortia were enriched on SAX from the same individual’s fecal microbiota across a one-month interval, suggesting that polysaccharide structure is more influential than stochastic alterations in microbiome composition in governing the outcomes of sequential batch cultivation experiments. SAX-consuming consortia were anchored by Bacteroides ovatus and retained diverse consortia of >12 OTUs; whereas final inulin-consuming consortia were dominated either by Klebsiella pneumoniae or Bifidobacterium sp. and Escherichia coli. Furthermore, auxotrophic interactions were less influential in structuring microbial consortia consuming SAX than the less-complex inulin. These data suggest that carbohydrate structural complexity affords independent niches that structure fermenting microbial consortia, whereas other metabolic interactions govern the composition of communities fermenting simpler carbohydrates.IMPORTANCEThe mechanisms by which gut microorganisms compete for and cooperate on human-indigestible carbohydrates of varying structural complexity remain unclear. Gaps in this understanding make it challenging to predict the effect of a particular dietary fiber’s structure on the diversity, composition, or function of gut microbiomes, especially with inter-individual variability in diets and microbiomes. Here, we demonstrate that carbohydrate structure governs the diversity of gut microbiota under high dilution pressure, suggesting that such structures may support microbial diversity in vivo. Further, we also demonstrate that carbohydrate polymers are not equivalent in the strength by which they influence community structure and function, and that metabolic interactions among members arising due to auxotrophy exert significant influence on the outcomes of these competitions for simpler polymers. Collectively, these data suggest that large, complex dietary fiber polysaccharides structure the human gut ecosystem in ways that smaller and simpler ones may not.

scholarly journals Autonomous and Assisted Control for Synthetic Microbiology

2020 ◽  
Vol 21 (23) ◽  
pp. 9223
Author(s):  
Alvaro Banderas ◽  
Matthias Le Bec ◽  
Céline Cordier ◽  
Pascal Hersen
Keyword(s):  
Robust Control ◽  
Population Level ◽  
Microbial Consortia ◽  
Intercellular Signaling ◽  
Biological Functions ◽  
External Perturbations ◽  
Experimental Approaches ◽  
And Control ◽  
Microbial Systems ◽  
External Computer

The control of microbes and microbial consortia to achieve specific functions requires synthetic circuits that can reliably cope with internal and external perturbations. Circuits that naturally evolved to regulate biological functions are frequently robust to alterations in their parameters. As the complexity of synthetic circuits increases, synthetic biologists need to implement such robust control “by design”. This is especially true for intercellular signaling circuits for synthetic consortia, where robustness is highly desirable, but its mechanisms remain unclear. Cybergenetics, the interface between synthetic biology and control theory, offers two approaches to this challenge: external (computer-aided) and internal (autonomous) control. Here, we review natural and synthetic microbial systems with robustness, and outline experimental approaches to implement such robust control in microbial consortia through population-level cybergenetics. We propose that harnessing natural intercellular circuit topologies with robust evolved functions can help to achieve similar robust control in synthetic intercellular circuits. A “hybrid biology” approach, where robust synthetic microbes interact with natural consortia and—additionally—with external computers, could become a useful tool for health and environmental applications.

scholarly journals Connecting structure and function from organisms to molecules in small animal symbioses through chemo-histo-tomography

2020 ◽  
Author(s):  
Benedikt Geier ◽  
Janina Oetjen ◽  
Bernhard Ruthensteiner ◽  
Maxim Polikarpov ◽  
Harald Gruber-Vodicka ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Mass Spectrometry Imaging ◽  
Natural Habitat ◽  
Anatomic Structure ◽  
X Ray ◽  
Culture Independent ◽  
Metabolic Interactions ◽  
Micro Organisms

AbstractOur understanding of metabolic interactions between small symbiotic animals and bacteria or parasitic eukaryotes that reside within their body is extremely limited. This gap in knowledge originates from a methodological challenge, namely to connect histological changes in host tissues induced by beneficial and parasitic (micro)organisms to the underlying metabolites. To close this gap, we developed chemo-histo-tomography (CHEMHIST), a culture-independent approach to connect anatomic structure and metabolic function in millimeter-sized symbiotic animals. CHEMHIST combines spatial metabolomics based on mass spectrometry imaging (MSI) and microanatomy-based micro-computed X-ray tomography (microCT) on the same animal. Both high-resolution MSI and microCT allowed us to correlate the distribution of metabolites to the same animal’s three-dimensional (3D) histology down to sub-micrometer resolutions. Our protocol is compatible with tissue specific DNA sequencing and fluorescence in situ hybridization (FISH) for the taxonomic identification and localization of the associated micro(organisms). Building CHEMHIST upon in situ imaging, we sampled an earthworm from its natural habitat and created an interactive 3D model of its physical and chemical interactions with bacteria and parasitic nematodes in its tissues. Combining MSI and microCT, we introduce a workflow to connect metabolic and anatomic phenotypes of small symbiotic animals that often represent keystone species for ecosystem-functioning.SignificanceMetabolites mediate the establishment and persistence of most inter-kingdom symbioses. Still, to pinpoint the metabolites each partner displays upon interaction remains the biggest challenge in studying multi-organismal assemblages. Addressing this challenge, we developed a correlative imaging workflow to connect the in situ production of metabolites with the organ-scale and cellular 3D distributions of mutualistic and pathogenic (micro)organisms in the same host animal. Combining mass spectrometry imaging and micro-computed X-ray tomography provided a culture-independent approach, which is essential to include the full spectrum of naturally occurring interactions. To introduce the potential of combining high-resolution tomography with metabolite imaging, we resolve the metabolic interactions between an invertebrate host, its symbiotic bacteria and tissue parasites at unprecedented detail for model and non-model symbioses.

scholarly journals Metabolic modeling of the International Space Station microbiome reveals key microbial interactions

2021 ◽  
Author(s):  
Rachita K Kumar ◽  
Nitin K Singh ◽  
Sanjaay Balakrishnan ◽  
Ceth W Parker ◽  
Karthik Raman ◽  
...  
Keyword(s):  
International Space Station ◽  
Space Station ◽  
Keystone Species ◽  
Microbial Interactions ◽  
Integrated Modelling ◽  
Klebsiella Pneumonia ◽  
Potential Contribution ◽  
International Space ◽  
Metabolic Interactions ◽  
Modelling Approach

Background: Recent studies have provided insights into the persistence and succession of microbes aboard the International Space Station (ISS), notably the dominance of Klebsiella pneumonia. However, the interactions between the various microbes aboard the ISS, and how it shapes the microbiome remain to be clearly understood. In this study, we apply a computational approach to predict possible metabolic interactions in the ISS microbiome and shed further light on its organization. Results: Through a combination of a systems-based graph-theoretical approach, and a constraint-based community metabolic modelling approach, we demonstrated several key interactions in the ISS microbiome. These complementary approaches provided insights into the metabolic interactions and dependencies present amongst various microbes in a community, highlighting key interactions and keystone species. Our results showed that the presence of K. pneumoniae is beneficial to many other microorganisms it coexists with, notably those from the Pantoea genus. Species belonging to the Enterobacteriaceae family were often found to be the most beneficial for the survival of other microorganisms in the ISS microbiome. However, K. pneumoniae was found to exhibit parasitic and amensalistic interactions with Aspergillus and Penicillium species, respectively. To prove this metabolic prediction, K. pneumoniae and Aspergillus fumigatus were co-cultured under normal and simulated microgravity, where K. pneumoniae cells showed parasitic characteristics to the fungus. The electron micrography revealed that the presence of K. pneumoniae compromised the morphology of fungal conidia and its biofilm biofilm-forming structures. Conclusions: Our study underscores the importance of K. pneumoniae in the ISS, and its potential contribution to the survival (mutualism) and eradication (parasitism) of other microbes, including potential pathogens. This integrated modelling approach, combined with experiments, demonstrates immense potential for understanding the organization of other such microbiomes, unravelling key organisms and their interdependencies.

scholarly journals The microbial consortia directed evolution towards plastic degradation – the key to waste management?

2019 ◽  
Vol 12 ◽  
pp. 2316-2319
Author(s):  
GURPREET KAUR SIDHU ◽  
Pooja Chandel
Keyword(s):  
Extended Period ◽  
Sole Source ◽  
Microbial Consortia ◽  
Hypothetical Proteins ◽  
Dumping Site ◽  
Domains Of Life ◽  
Plastic Degradation ◽  
Basal Media ◽  
Micro Organisms ◽  
Current Report

The rampant use of plastics and their disposal into waste are adding to the problems of pollution. The resistance of plastics to bio-degradation is an added advantage for its significant use but the same property creates havoc when the plastic products are disposed off as waste in massive amounts. The property of micro-organisms to evolve quickly brings answers to even the most impossible situations. The current and several other reports show that the plastic is bio-degradable. The current report shows the action of consortia of microbes isolated from a plastic dumping site can lead to degradation of the polymer. The microbial consortia isolated from plastic dumping site when made to grow in controlled conditions in presence of basal media with plastic as sole source of carbon for an extended period of time, aberrations were observed on surface of the plastic. The proteins reported till date in plastic degradation when analysed in-silico for their homologs in all domains of life, they were found to be significantly similar to proteins of cutinase, hydrolase, lipase and some hypothetical proteins. This shows that the plastic degrading proteins have possibly evolved from these protein families.

Effect of Interaction between Earthworm and Microbes on the Degradation Time of Agro-Waste

2013 ◽  
Vol 295-298 ◽  
pp. 1710-1713
Author(s):  
Shahul Hamid Fauziah ◽  
Chijioke Uche Emenike ◽  
Periatamby Agamuthu
Keyword(s):  
Weight Loss ◽  
Sugarcane Bagasse ◽  
Microbial Consortia ◽  
Available Phosphorus ◽  
Biological Processes ◽  
Eudrilus Eugeniae ◽  
Ph Values ◽  
Micro Organisms ◽  
Degradation Time ◽  
Reduced Time

Impact of macro-organisms in biological processes had been considerably studied but some of the discrete interactions that exist between macro- and micro-organisms still remain complex and sometimes elusive. Agro-waste is a type of waste that remains highly inevitable in our society and its disposal is a subject of concern. Therefore, this study aimed to degrade sugarcane bagasse which is a significant agro-waste in Malaysia, while trying to understand the interaction between microbes and earthworm utilized in the bioprocess. Sugarcane bagasse was blended with spent tea in equal ratio before composting with the aid of Eudrilus eugeniae and introduced microbial consortia. Though varied, pH values across the amendments tended towards alkaline state, just as the available Phosphorus (P) and exchangeable Potassium (K) increased in the value. Total organic carbon (TOC) across the amendments showed reduction in value; 47% in TS (tea and sugarcane bagasse), whereas 25% in TS6M (Tea + sugarcane bagasse + 6 microbes) and 68% in TS3M (tea bagasse + 3 microbes). However, weight loss in Eudrilus eugeinae was found to be proportional to the reduced time of degradation. TS3M at 33% worm weight loss was recorded at 11 day degradation time, than TS6M (27%) and TS (16%) that showed 13 and 20 days degradation time respectively. Weight loss in earthworm is correlated with microbial interaction and can be a reflection of rate decomposition of organic components of agro-waste in a vermicomposting process.

scholarly journals Metabolic interactions between Toxoplasma gondii and its host

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1719 ◽  
Author(s):  
Martin Blume ◽  
Frank Seeber
Keyword(s):  
Toxoplasma Gondii ◽  
Host Cell ◽  
Chronic Infection ◽  
Current Status ◽  
Obligate Intracellular ◽  
Obligate Intracellular Parasite ◽  
Open Questions ◽  
Metabolic Interactions ◽  
Experimental Approaches ◽  
Host Parasite

Toxoplasma gondii is an obligate intracellular parasite belonging to the phylum Apicomplexa that infects all warm-blooded animals, including humans. T. gondii can replicate in every nucleated host cell by orchestrating metabolic interactions to derive crucial nutrients. In this review, we summarize the current status of known metabolic interactions of T. gondii with its host cell and discuss open questions and promising experimental approaches that will allow further dissection of the host–parasite interface and discovery of ways to efficiently target both tachyzoite and bradyzoite forms of T. gondii, which are associated with acute and chronic infection, respectively.

scholarly journals Metabolically cohesive microbial consortia and ecosystem functioning

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190245 ◽  
Author(s):  
Alberto Pascual-García ◽  
Sebastian Bonhoeffer ◽  
Thomas Bell
Keyword(s):  
Ecosystem Functioning ◽  
Microbial Consortia ◽  
Recent Theory ◽  
Microbial Community Ecology ◽  
In The Wild ◽  
Ecosystem Level ◽  
Metabolic Interactions ◽  
Evolutionary Consequences ◽  
Competition For Resources ◽  
Theory And Experiments

Recent theory and experiments have reported a reproducible tendency for the coexistence of microbial species under controlled environmental conditions. This observation has been explained in the context of competition for resources and metabolic complementarity given that, in microbial communities (MCs), many excreted by-products of metabolism may also be resources. MCs therefore play a key role in promoting their own stability and in shaping the niches of the constituent taxa. We suggest that an intermediate level of organization between the species and the community level may be pervasive, where tightly knit metabolic interactions create discrete consortia that are stably maintained. We call these units Metabolically Cohesive Consortia (MeCoCos) and we discuss the environmental context in which we expect their formation, and the ecological and evolutionary consequences of their existence. We argue that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for our understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

Sign in / Sign up

Export Citation Format

Share Document