scholarly journals Microbial species coexistence depends on the host environment

2019 ◽  
Author(s):  
Peter Deines ◽  
Katrin Hammerschmidt ◽  
Thomas CG Bosch
Keyword(s):  
Community Composition ◽  
Carrying Capacity ◽  
Species Coexistence ◽  
Bacterial Species ◽  
Microbial Interactions ◽  
Native Community ◽  
Host Environment ◽  
Microbial Species ◽  
Initial Starting

AbstractOrganisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germ free hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial structure of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the fractions of both species on the host do not match the fractions reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that the rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems.ImportanceThis work studies microbial interactions within the microbiome of the simple cnidarian, Hydra, and investigates whether microbial species coexistence and community stability depends on the host environment. We find that the outcome of the interaction between the two most dominant bacterial species in Hydra’s microbiome differs depending on the environment and only results in a stable coexistence in the host context. The interactive ecology between the host, the two most dominant microbes, but also the less abundant members of the microbiome, are critically important for achieving the native community composition. This indicates that the metaorganism environment needs to be taken into account when studying microbial interactions.

scholarly journals Microbial Species Coexistence Depends on the Host Environment

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Peter Deines ◽  
Katrin Hammerschmidt ◽  
Thomas C. G. Bosch
Keyword(s):  
Community Composition ◽  
Carrying Capacity ◽  
Species Coexistence ◽  
Bacterial Species ◽  
Microbial Interactions ◽  
Native Community ◽  
Host Environment ◽  
Microbial Species ◽  
Relative Abundances

ABSTRACT Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germfree hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial distribution of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the relative abundances of both species on the host do not match the relative abundances reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems. IMPORTANCE This work studies microbial interactions within the microbiome of the simple cnidarian Hydra and investigates whether microbial species coexistence and community stability depend on the host environment. We find that the outcome of the interaction between the two most dominant bacterial species in Hydra’s microbiome differs depending on the environment and results in a stable coexistence only in the host context. The interactive ecology between the host and the two most dominant microbes, but also the less abundant members of the microbiome, is critically important for achieving the native community composition. This indicates that the metaorganism environment needs to be taken into account when studying microbial interactions.

scholarly journals Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species

2020 ◽  
Author(s):  
Tony J. Lam ◽  
Moses Stamboulian ◽  
Wontack Han ◽  
Yuzhen Ye
Keyword(s):  
Microbial Communities ◽  
Bacterial Species ◽  
Microbial Interactions ◽  
Phylogenetic Distance ◽  
Phylogenetic Relatedness ◽  
Bacterial Interactions ◽  
Competition And Cooperation ◽  
Microbial Species ◽  
Metabolic Interactions ◽  
Genome Scale

AbstractMicrobial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of metabolic interactions, such as competition and cooperation, between bacterial species. By nature, phylogenetically similar microbial species are likely to share common functional profiles or biological pathways due to their genomics similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation based on functional/pathway profiles may bias downstream applications.To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.Author summaryMicrobial communities, also known as microbiomes, are formed through the interactions of various microbial species. Utilizing genomic sequencing, it is possible to infer the compositional make-up of communities as well as predict their metabolic interactions. However, because some species are more similarly related to each other, while others are more distantly related, one cannot directly compare metabolic relationships without first accounting for their phylogenetic relatedness. Here we developed a computational pipeline which predicts complimentary and competitive metabolic relationships between bacterial species, while normalizing for their phylogenetic relatedness. Our results show that phylogenetic distances are correlated with metabolic interactions, and factoring out such relationships can help better understand microbial interactions which drive community formation.

scholarly journals Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species

2020 ◽  
Vol 16 (10) ◽  
pp. e1007951
Author(s):  
Tony J. Lam ◽  
Moses Stamboulian ◽  
Wontack Han ◽  
Yuzhen Ye
Keyword(s):  
Dominant Role ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Interactions ◽  
Phylogenetic Distance ◽  
Metabolic Cooperation ◽  
Bacterial Interactions ◽  
Microbial Species ◽  
Metabolic Models ◽  
Genome Scale

Microbial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of cooperative and competitive metabolic interactions between bacterial species. By nature, phylogenetically similar microbial species are more likely to share common functional profiles or biological pathways due to their genomic similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation between species based on functional/pathway profiles may bias downstream applications. To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut associated bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.

scholarly journals Erratum for Deines et al., “Microbial Species Coexistence Depends on the Host Environment”

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Peter Deines ◽  
Katrin Hammerschmidt ◽  
Thomas C. G. Bosch
Keyword(s):  
Species Coexistence ◽  
Host Environment ◽  
Microbial Species

Production of Novel Bioactive Compounds by the Bacteria Associated with Some Marine Sponges of Gulf of Mannar and Palk Bay, Southeast Coast of India

2018 ◽  
Vol 6 (8) ◽  
pp. 183
Author(s):  
V. Ramadas ◽  
G. Chandralega
Keyword(s):  
Bioactive Compounds ◽  
Bacterial Species ◽  
Marine Sponges ◽  
Marine Organisms ◽  
Gulf Of Mannar ◽  
Bacterial Symbionts ◽  
Palk Bay ◽  
Excellent Source

Sponges, exclusively are aquatic and mostly marine, are found from the deepest oceans to the edge of the sea. There are approximately 15,000 species of sponges in the world, of which, 150 occur in freshwater, but only about 17 are of commercial value. A total of 486 species of sponges have been identified in India. In the Gulf of Mannar and Palk Bay a maximum of 319 species of sponges have been recorded. It has been proved that marine organisms are excellent source of bioactive secondary metabolites and number of compounds of originated from marine organisms had been reported to possess in-vitro and in-vivo immuno stimulatory activity. Extracts from 20 sponge species were tested for bacterial symbionts and bioactive compounds were isolated from such associated bacterial species in the present study.

Molecular Detection of Bacterial Pathogens Directly from the Nasal Swabs and Lung Tissue of Sheep and Goats

2019 ◽  
Vol 15 (02) ◽  
pp. 22-25
Author(s):  
Sunaina Thakur ◽  
Subhash Verma ◽  
Prasenjit Dhar ◽  
Mandeep Sharma
Keyword(s):  
Pasteurella Multocida ◽  
Direct Detection ◽  
Bacterial Species ◽  
Economic Losses ◽  
Isolation And Identification ◽  
Sheep And Goats ◽  
Histophilus Somni ◽  
Nasal Swabs ◽  
Mycoplasma Spp

Respiratory infections of sheep and goats cause heavy morbidity and mortality, leading to huge economic losses. Conventional methods of diagnosis that include isolation and identification of incriminating microbes are time-consuming and fraught with logistic challenges. Direct detection of incriminating microbes using molecular tools is gaining popularity in clinical, microbiological settings. In this study, a total of 50 samples (44 nasal swabs and 6 lung tissues) from sheep and goats were screened for the detection of different bacterial species by in vitro amplification of genus or species-specific genes. Histophilus somni was detected in 2% goat samples, Trueperella pyogenes in 20% goat nasal swabs, whereas 22% goat nasal swab samples were found positive for Mycoplasma spp. None of the samples from sheep was detected positive for H. somni, T. pyogenes, Mycoplasma spp. Similarly, all samples, irrespective, whether from sheep or goats, showed negative results for Pasteurella multocida, Mannheimia haemolytica, and Corynebacterium pseudotuberculosis.

scholarly journals Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate

2014 ◽  
Vol 81 (1) ◽  
pp. 130-138 ◽  
Author(s):  
James Kirby ◽  
Minobu Nishimoto ◽  
Ruthie W. N. Chow ◽  
Edward E. K. Baidoo ◽  
George Wang ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Xylose Reductase ◽  
Pentose Phosphate ◽  
Terpene Biosynthesis ◽  
Content Type ◽  
E Coli ◽  
Pathway Expression ◽  
Terpene Synthesis ◽  
Selection For

ABSTRACTTerpene synthesis in the majority of bacterial species, together with plant plastids, takes place via the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway. The first step of this pathway involves the condensation of pyruvate and glyceraldehyde 3-phosphate by DXP synthase (Dxs), with one-sixth of the carbon lost as CO2. A hypothetical novel route from a pentose phosphate to DXP (nDXP) could enable a more direct pathway from C5sugars to terpenes and also circumvent regulatory mechanisms that control Dxs, but there is no enzyme known that can convert a sugar into its 1-deoxy equivalent. Employing a selection for complementation of adxsdeletion inEscherichia coligrown on xylose as the sole carbon source, we uncovered two candidate nDXP genes. Complementation was achieved either via overexpression of the wild-typeE. coliyajOgene, annotated as a putative xylose reductase, or via various mutations in the nativeribBgene.In vitroanalysis performed with purified YajO and mutant RibB proteins revealed that DXP was synthesized in both cases from ribulose 5-phosphate (Ru5P). We demonstrate the utility of these genes for microbial terpene biosynthesis by engineering the DXP pathway inE. colifor production of the sesquiterpene bisabolene, a candidate biodiesel. To further improve flux into the pathway from Ru5P, nDXP enzymes were expressed as fusions to DXP reductase (Dxr), the second enzyme in the DXP pathway. Expression of a Dxr-RibB(G108S) fusion improved bisabolene titers more than 4-fold and alleviated accumulation of intracellular DXP.

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