scholarly journals Quantifying multi-species microbial interactions in the larval zebrafish gut

2020 ◽  
Author(s):  
Deepika Sundarraman ◽  
Edouard A. Hay ◽  
Dylan M. Martins ◽  
Drew S. Shields ◽  
Noah L. Pettinari ◽  
...  
Keyword(s):  
Species Interactions ◽  
Bacterial Species ◽  
Higher Order ◽  
Microbial Interactions ◽  
Microbial Composition ◽  
Intestinal Microbes ◽  
Larval Zebrafish ◽  
Species Abundances ◽  
Health And Disease ◽  
Multiple Species

AbstractThe microbial communities resident in animal intestines are composed of multiple species that together play important roles in host development, health and disease. Due to the complexity of these communities and the difficulty of characterizing them in situ, the determinants of microbial composition remain largely unknown. Further, it is unclear for many multi-species consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions, or whether higher-order interactions are needed to explain emergent compositions. To address this, we examine commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. Using a dissection and plating assay, we demonstrate the construction of communities of one to five bacterial species and show that the outcomes from the two-species competitions fail to predict species abundances in more complex communities. With multiple species present, inter-bacterial interactions become weaker and more cooperative, suggesting that higher-order interactions in the vertebrate gut may stabilize complex communities.

scholarly journals Higher-Order Interactions Dampen Pairwise Competition in the Zebrafish Gut Microbiome

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Deepika Sundarraman ◽  
Edouard A. Hay ◽  
Dylan M. Martins ◽  
Drew S. Shields ◽  
Noah L. Pettinari ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Species Interactions ◽  
Bacterial Species ◽  
Higher Order ◽  
Microbial Composition ◽  
Intestinal Microbes ◽  
Larval Zebrafish ◽  
Microbial Species ◽  
Species Abundances ◽  
Multiple Species

ABSTRACT The microbial communities resident in animal intestines are composed of multiple species that together play important roles in host development, health, and disease. Due to the complexity of these communities and the difficulty of characterizing them in situ, the determinants of microbial composition remain largely unknown. Further, it is unclear for many multispecies consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions or whether higher-order interactions are needed to explain emergent compositions. To address this, we examine commensal intestinal microbes in larval zebrafish, initially raised germfree, to allow the introduction of controlled combinations of bacterial species. Using a dissection and plating assay, we demonstrate the construction of communities of one to five bacterial species and show that the outcomes from the two-species competitions fail to predict species abundances in more complex communities. With multiple species present, interbacterial interactions become weaker, suggesting that higher-order interactions in the vertebrate gut stabilize complex communities. IMPORTANCE Understanding the rules governing the composition of the diverse microbial communities that reside in the vertebrate gut environment will enhance our ability to manipulate such communities for therapeutic ends. Synthetic microbial communities, assembled from specific combinations of microbial species in germfree animals, allow investigation of the fundamental question of whether multispecies community composition can be predicted solely based on the combined effects of interactions between pairs of species. If so, such predictability would enable the construction of communities with desired species from the bottom up. If not, the apparent higher-order interactions imply that emergent community-level characteristics are crucial. Our findings using up to five coexisting native bacterial species in larval zebrafish, a model vertebrate, provide experimental evidence for higher-order interactions and, moreover, show that these interactions promote the coexistence of microbial species in the gut.

scholarly journals Aridity weakens population-level effects of multiple species interactions on Hibiscus meyeri

2017 ◽  
Vol 115 (3) ◽  
pp. 543-548 ◽  
Author(s):  
Allison M. Louthan ◽  
Robert M. Pringle ◽  
Jacob R. Goheen ◽  
Todd M. Palmer ◽  
William F. Morris ◽  
...  
Keyword(s):  
Population Growth ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Population Level ◽  
Distinct Species ◽  
High Elevation ◽  
Relative Strength ◽  
Herbaceous Plant ◽  
Species Abundances ◽  
Multiple Species

Predicting how species’ abundances and ranges will shift in response to climate change requires a mechanistic understanding of how multiple factors interact to limit population growth. Both abiotic stress and species interactions can limit populations and potentially set range boundaries, but we have a poor understanding of when and where each is most critical. A commonly cited hypothesis, first proposed by Darwin, posits that abiotic factors (e.g., temperature, precipitation) are stronger determinants of range boundaries in apparently abiotically stressful areas (“stress” indicates abiotic factors that reduce population growth), including desert, polar, or high-elevation environments, whereas species interactions (e.g., herbivory, competition) play a stronger role in apparently less stressful environments. We tested a core tenet of this hypothesis—that population growth rate is more strongly affected by species interactions in less stressful areas—using experimental manipulations of species interactions affecting a common herbaceous plant, Hibiscus meyeri (Malvaceae), across an aridity gradient in a semiarid African savanna. Population growth was more strongly affected by four distinct species interactions (competition with herbaceous and shrubby neighbors, herbivory, and pollination) in less stressful mesic areas than in more stressful arid sites. However, contrary to common assumptions, this effect did not arise because of greater density or diversity of interacting species in less stressful areas, but rather because aridity reduced sensitivity of population growth to these interactions. Our work supports classic predictions about the relative strength of factors regulating population growth across stress gradients, but suggests that this pattern results from a previously unappreciated mechanism that may apply to many species worldwide.

scholarly journals Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions

Nutrients ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 467 ◽  
Author(s):  
Yanbei Wu ◽  
Robert Li ◽  
Haiqiu Huang ◽  
Arnetta Fletcher ◽  
Lu Yu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Tumor Growth ◽  
Gut Microbiome ◽  
Species Interactions ◽  
Tumor Development ◽  
Xenograft Model ◽  
Microbial Interactions ◽  
Control Group ◽  
Rrna Gene ◽  
Microbial Composition

Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks. The effects of dietary I3C on gut microbial composition and microbial species interactions were then examined by 16s rRNA gene-based sequencing and co-occurrence network analysis. I3C supplementation significantly inhibited tumor growth (p < 0.0001) and altered the structure of gut microbiome. The abundance of the phylum Deferribacteres, more specifically, Mucispirillum schaedleri, was significantly increased by dietary I3C. Additionally, I3C consumption also changed gut microbial co-occurrence patterns. One of the network modules in the control group, consisting of seven bacteria in family S-27, was positively correlated with tumor size (p < 0.009). Moreover, dietary I3C disrupted microbial interactions and altered this association between specific microbial network and tumor development. Our results unraveled complex relationships among I3C ingestion, gut microbiota, and prostate tumor development and may provide a novel insight into the mechanism for the chemopreventive effect of dietary I3C on prostate cancer.

scholarly journals Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Marika Ziesack ◽  
Travis Gibson ◽  
John K. W. Oliver ◽  
Andrew M. Shumaker ◽  
Bryan B. Hsu ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Consortium ◽  
Microbial Interactions ◽  
Environmental Benefits ◽  
Microbial Consortia ◽  
Positive Interactions ◽  
Complex Environments ◽  
Bacterial Consortia ◽  
Health And Disease ◽  
Antagonistic Interactions

ABSTRACT In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments. IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.

scholarly journals Engineered inter-species amino acid cross-feeding increases population evenness in a synthetic bacterial consortium

2018 ◽  
Author(s):  
Marika Ziesack ◽  
Travis Gibson ◽  
John K.W. Oliver ◽  
Andrew M. Shumaker ◽  
Bryan B. Hsu ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Consortium ◽  
Microbial Interactions ◽  
Environmental Benefits ◽  
Microbial Consortia ◽  
Positive Interactions ◽  
Complex Environments ◽  
Bacterial Consortia ◽  
Health And Disease ◽  
Antagonistic Interactions

AbstractIn nature, microbes interact antagonistically, neutrally or beneficially. To shed light on the effects of positive interactions in microbial consortia we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wildtype consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.ImportanceMicrobial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortia function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.

scholarly journals Dietary Curdlan Enhances Bifidobacteria and Reduces Intestinal Inflammation in Mice

Nutrients ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 1305
Author(s):  
Shafaque Rahman ◽  
Mark Davids ◽  
Patricia H. P. van Hamersveld ◽  
Olaf Welting ◽  
Hakim Rahaoui ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Intestinal Inflammation ◽  
Alcaligenes Faecalis ◽  
Food Additive ◽  
Microbial Interactions ◽  
Oral Gavage ◽  
Microbial Composition ◽  
Colonic Inflammation ◽  
Intestinal Microbes ◽  
Human Intestinal Microbiota

β-glucan consumption is known for its beneficial health effects, but the mode of action is unclear. While humans and mice lack the required enzymes to digest β-glucans, certain intestinal microbes can digest β-glucans, triggering gut microbial changes. Curdlan, a particulate β-glucan isolated from Alcaligenes faecalis, is used as a food additive. In this study we determined the effect of curdlan intake in mice on the intestinal microbiota and dextran sodium sulfate (DSS)-induced intestinal inflammation. The effect of curdlan on the human intestinal microbiota was assessed using i-screen, an assay for studying anaerobic microbial interactions. Mice received oral gavage with vehicle or curdlan for 14 days followed by DSS for 7 days. The curdlan-fed group showed reduced weight loss and colonic inflammation compared to the vehicle-fed group. Curdlan intake did not induce general microbiota community changes, although a specific Bifidobacterium, closely related to Bifidobacterium choerinum, was observed to be 10- to 100-fold more prevalent in the curdlan-fed group under control and colitis conditions, respectively. When tested in i-screen, curdlan induced a global change in the microbial composition of the healthy intestinal microbiota from a human. Overall, these results suggest that dietary curdlan induces microbiota changes that could reduce intestinal inflammation.

scholarly journals Monoassociation with bacterial isolates reveals the role of colonization, community complexity and abundance on locomotor behavior in larval zebrafish

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Chelsea A. Weitekamp ◽  
Allison Kvasnicka ◽  
Scott P. Keely ◽  
Nichole E. Brinkman ◽  
Xia Meng Howey ◽  
...  
Keyword(s):  
Total Concentration ◽  
Bacterial Species ◽  
Locomotor Behavior ◽  
Host Cells ◽  
Individual Species ◽  
Zebrafish Model ◽  
Associated Bacteria ◽  
Larval Zebrafish ◽  
Toxicological Studies ◽  
Community Complexity

Abstract Background Across taxa, animals with depleted intestinal microbiomes show disrupted behavioral phenotypes. Axenic (i.e., microbe-free) mice, zebrafish, and fruit flies exhibit increased locomotor behavior, or hyperactivity. The mechanism through which bacteria interact with host cells to trigger normal neurobehavioral development in larval zebrafish is not well understood. Here, we monoassociated zebrafish with either one of six different zebrafish-associated bacteria, mixtures of these host-associates, or with an environmental bacterial isolate. Results As predicted, the axenic cohort was hyperactive. Monoassociation with three different host-associated bacterial species, as well as with the mixtures, resulted in control-like locomotor behavior. Monoassociation with one host-associate and the environmental isolate resulted in the hyperactive phenotype characteristic of axenic larvae, while monoassociation with two other host-associated bacteria partially blocked this phenotype. Furthermore, we found an inverse relationship between the total concentration of bacteria per larvae and locomotor behavior. Lastly, in the axenic and associated cohorts, but not in the larvae with complex communities, we detected unexpected bacteria, some of which may be present as facultative predators. Conclusions These data support a growing body of evidence that individual species of bacteria can have different effects on host behavior, potentially related to their success at intestinal colonization. Specific to the zebrafish model, our results suggest that differences in the composition of microbes in fish facilities could affect the results of behavioral assays within pharmacological and toxicological studies.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anna Detman ◽  
Michał Bucha ◽  
Laura Treu ◽  
Aleksandra Chojnacka ◽  
Łukasz Pleśniak ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
Bacterial Species ◽  
Stable Carbon Isotope ◽  
Anaerobic Sludge ◽  
Methane Formation ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Core Microbiome ◽  
Specific Species

Abstract Background During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. Results Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%–67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. Conclusions In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

scholarly journals Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome

2021 ◽  
Author(s):  
Melanie R. Smee ◽  
Sally A. Raines ◽  
Julia Ferrari
Keyword(s):  
Species Interactions ◽  
Acyrthosiphon Pisum ◽  
Parasitoid Wasp ◽  
Extensive Study ◽  
Genetic Identity ◽  
Host Genotype ◽  
Species Identity ◽  
Microbial Symbionts ◽  
And Performance ◽  
Multiple Species

AbstractMicrobial symbionts often alter the phenotype of their host. Benefits and costs to hosts depend on many factors, including host genotype, symbiont species and genotype, and environmental conditions. Here, we present a study demonstrating genotype-by-genotype (G×G) interactions between multiple species of endosymbionts harboured by an insect, and the first to quantify the relative importance of G×G interactions compared with species interactions in such systems. In the most extensive study to date, we microinjected all possible combinations of five Hamiltonella defensa and five Fukatsuia symbiotica (X-type; PAXS) isolates into the pea aphid, Acyrthosiphon pisum. We applied several ecological challenges: a parasitoid wasp, a fungal pathogen, heat shock, and performance on different host plants. Surprisingly, genetic identity and genotype × genotype interactions explained far more of the phenotypic variation (on average 22% and 31% respectively) than species identity or species interactions (on average 12% and 0.4%, respectively). We determined the costs and benefits associated with co-infection, and how these compared to corresponding single infections. All phenotypes were highly reliant on individual isolates or interactions between isolates of the co-infecting partners. Our findings highlight the importance of exploring the eco-evolutionary consequences of these highly specific interactions in communities of co-inherited species.

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