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Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions

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A special issue of Microorganisms (ISSN 2076-2607).

Deadline for manuscript submissions: closed (30 November 2020) | Viewed by 33057

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Dr. Nicolas Derome

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Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
Interests: host-microbiota interactions in animals (mostly fish and honeybees, both in controlled and natural populations); microbiota ontogeny; aquaculture; probiotics; molecular evolution; functional metagenomics; microbial ecology; bioinformatics

Special Issue Information

Dear Colleagues,

In recent decades, microbiota-focused research on animal models has paved the way to developing a highly integrated approach to understand complex relationships between the host organism and both its associated and environmental microbial communities. Most importantly, the recent development of high-throughput sequencing technologies, combined with the rise of bioinformatics, has raised the curtain on an unsuspected microbial diversity, both in terms of taxonomy and functions, from highly extreme environments to host tissues previously thought of as sterile. Furthermore, animal models have revealed tight functional interactions between the host and their microbiota, such as regulating the metabolism, immune system maturation, and via the vagus nerve, brain development, and various behaviors. Awareness of the fact that microbiota extensively contribute to host biology has led the scientific community to rethink the study of any organism in a much more integrated way. These significant advances in the field of host–microbiota symbioses has led researchers to adapt the Holobiont concept formalized by Lynn Margulis (1993), which considers the host–microbiota system as a whole organism which, in light of the rise of metagenomics, was then viewed as a single unit of selection, as formally described in the hologenome (i.e., host genome + associated microbial genomes) concept by Richard Jefferson (1994) and later by Zilber-Rosenberg (2008). The most recent advances in animal microbiota studies shed a light on the fact that host–microbiota beneficial interactions can be broken by multiple stressors (including unbalanced nutrition), allowing opportunistic microbial strains to induce negative effects on the host, including physiological disturbances on neuroendocrine functions and epigenetics modifications.Overall, current research on animal microbiota focuses on integrative studies of gene-diet-microbiota interactions in order to tightly disentangle factors that influence host development. The outcomes are not only beneficial for the sustainability of the agrifood industry but also by revolutionizing personalized medicine.

Dr. Nicolas Derome
Guest Editor

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Published Papers (7 papers)

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Research

14 pages, 1905 KiB

Open AccessArticle

Differing Dietary Nutrients and Diet-Associated Bacteria Has Limited Impact on Spider Gut Microbiota Composition

by Wang Zhang, Fengjie Liu, Yang Zhu, Runhua Han, Letian Xu and Jie Liu

Microorganisms 2021, 9(11), 2358; https://doi.org/10.3390/microorganisms9112358 - 15 Nov 2021

Cited by 2 | Viewed by 2454

Abstract

Spiders are a key predator of insects across ecosystems and possess great potential as pest control agents. Unfortunately, it is difficult to artificially cultivate multiple generations of most spider species. Since gut bacterial flora has been shown to significantly alter nutrient availability, it is plausible that the spiders’ microbial community plays a key role in their unsuccessful breeding. However, both the gut microbial composition and its influencing factors in many spiders remain a mystery. In this study, the gut microbiota of Campanicola campanulata, specialists who prey on ants and are widely distributed across China, was characterized. After, the impact of diet and diet-associated bacteria on gut bacterial composition was evaluated. First, two species of prey ants (Lasius niger and Tetramorium caespitum) were collected from different locations and fed to C. campanulata. For each diet, we then profiled the nutritional content of the ants, as well as the bacterial communities of both the ants and spiders. Results showed that the protein and carbohydrate content varied between the two prey ant species. We isolated 682 genera from 356 families in the ants (dominant genera including Pseudomonas, Acinetobacter, Paraburkholderia, Staphylococcus, and Novosphingobium), and 456 genera from 258 families in the spiders (dominated by Pseudomonas). However, no significant differences were found in the gut microbiota of spiders that were fed the differing ants. Together, these results indicate that nutritional variation and diet-associated bacterial differences have a limited impact on the microbial composition of spider guts, highlighting that spiders may have a potentially stable internal environment and lay the foundation for future investigations into gut microbiota. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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20 pages, 6108 KiB

Open AccessArticle

Configuration of Gut Microbiota Structure and Potential Functionality in Two Teleosts under the Influence of Dietary Insect Meals

by Nikolas Panteli, Maria Mastoraki, Maria Lazarina, Stavros Chatzifotis, Eleni Mente, Konstantinos Ar. Kormas and Efthimia Antonopoulou

Microorganisms 2021, 9(4), 699; https://doi.org/10.3390/microorganisms9040699 - 28 Mar 2021

Cited by 38 | Viewed by 5554

Abstract

Insect meals are considered promising, eco-friendly, alternative ingredients for aquafeed. Considering the dietary influence on establishment of functioning gut microbiota, the effect of the insect meal diets on the microbial ecology should be addressed. The present study assessed diet- and species-specific shifts in gut resident bacterial communities of juvenile reared Dicentrarchus labrax and Sparus aurata in response to three experimental diets with insect meals from three insects (Hermetia illucens, Tenebrio molitor, Musca domestica), using high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene. The dominant phyla were Firmicutes, Proteobacteria and Actinobacteria in all dietary treatments. Anaerococcus sp., Cutibacterium sp. and Pseudomonas sp. in D. labrax, and Staphylococcus sp., Hafnia sp. and Aeromonas sp. in S. aurata were the most enriched shared species, following insect-meal inclusion. Network analysis of the dietary treatments highlighted diet-induced changes in the microbial community assemblies and revealed unique and shared microbe-to-microbe interactions. PICRUSt-predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly differentiated, including genes associated with metabolic pathways. The present findings strengthen the importance of diet in microbiota configuration and underline that different insects as fish feed ingredients elicit species-specific differential responses of structural and functional dynamics in gut microbial communities. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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14 pages, 2161 KiB

Open AccessArticle

Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod

by Marius Bredon, Elisabeth Depuydt, Lucas Brisson, Laurent Moulin, Ciriac Charles, Sophie Haenn, Bouziane Moumen and Didier Bouchon

Microorganisms 2021, 9(1), 148; https://doi.org/10.3390/microorganisms9010148 - 11 Jan 2021

Cited by 5 | Viewed by 3444

Abstract

The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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13 pages, 1733 KiB

Open AccessArticle

Isolation of Phaeobacter sp. from Larvae of Atlantic Bonito (Sarda sarda) in a Mesocosmos Unit, and Its Use for the Rearing of European Seabass Larvae (Dicentrarchus labrax L.)

by Pavlos Makridis, Fotini Kokou, Christos Bournakas, Nikos Papandroulakis and Elena Sarropoulou

Microorganisms 2021, 9(1), 128; https://doi.org/10.3390/microorganisms9010128 - 8 Jan 2021

Cited by 17 | Viewed by 3067

Abstract

The target of this study was to use indigenous probiotic bacteria in the rearing of seabass larvae. A Phaeobacter sp. strain isolated from bonito yolk-sac larvae (Sarda sarda) and identified by amplification of 16S rDNA showed in vitro inhibition against Vibrio anguillarum. This Phaeobacter sp. strain was used in the rearing of seabass larvae (Dicentrarchus labrax L.) in a large-scale trial. The survival of seabass after 60 days of rearing and the specific growth rate at the late exponential growth phase were significantly higher in the treatment receiving probiotics (p < 0.05). Microbial community richness as determined by denaturing gradient gel electrophoresis (DGGE) showed an increase in bacterial diversity with fish development. Changes associated with the administration of probiotics were observed 11 and 18 days after hatching but were not apparent after probiotic administration stopped. In a small challenge experiment, seabass larvae from probiotic treatment showed increased survival (p < 0.05) after experimental infection with a mild pathogen (Vibrio harveyi). Overall, our results showed that the use of an indigenous probiotic strain had a beneficial impact on larval rearing in industry-like conditions. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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18 pages, 399 KiB

Open AccessArticle

Effects of Thermal Stress on the Gut Microbiome of Juvenile Milkfish (Chanos chanos)

by Christiane Hassenrück, Hannes Reinwald, Andreas Kunzmann, Inken Tiedemann and Astrid Gärdes

Microorganisms 2021, 9(1), 5; https://doi.org/10.3390/microorganisms9010005 - 22 Dec 2020

Cited by 35 | Viewed by 5828

Abstract

Milkfish, an important aquaculture species in Asian countries, are traditionally cultured in outdoor-based systems. There, they experience potentially stressful fluctuations in environmental conditions, such as temperature, eliciting changes in fish physiology. While the importance of the gut microbiome for the welfare and performance of fish has been recognized, little is known about the effects of thermal stress on the gut microbiome of milkfish and its interactions with the host’s metabolism. We investigated the gut microbiome of juvenile milkfish in a thermal stress experiment, comparing control (26 °C) and elevated temperature (33 °C) treatments over three weeks, analyzing physiological biomarkers, gut microbiome composition, and tank water microbial communities using 16S amplicon sequencing. The gut microbiome was distinct from the tank water and dominated by Cetobacterium, Enterovibrio, and Vibrio. We observed a parallel succession in both temperature treatments, with microbial communities at 33 °C differing more strongly from the control after the initial temperature increase and becoming more similar towards the end of the experiment. As proxy for the fish’s energy status, HSI (hepatosomatic index) was correlated with gut microbiome composition. Our study showed that thermal stress induced changes in the milkfish gut microbiome, which may contribute to the host’s habituation to elevated temperatures over time. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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9 pages, 956 KiB

Open AccessArticle

Siccibacter turicensis from Kangaroo Scats: Possible Implication in Cellulose Digestion

by Sudip Dhakal, Jarryd M. Boath, Thi Thu Hao Van, Robert J. Moore and Ian G. Macreadie

Microorganisms 2020, 8(5), 635; https://doi.org/10.3390/microorganisms8050635 - 27 Apr 2020

Cited by 8 | Viewed by 3839

Abstract

Microbiota in the kangaroo gut degrade cellulose, contributing to the kangaroo’s energy and survival. In this preliminary study, to discover more about the gut microbes that contribute to the survival of kangaroos, cellulose-degrading bacteria were isolated from kangaroo scats by selection on solidified media containing carboxymethyl cellulose as the main carbon source. One frequently occurring aerobic bacterium was Siccibacter turicensis, a microbe previously isolated in fruit powder and from a patient with angular cheilitis. The whole genome sequence of the kangaroo isolate was obtained using the Illumina MiSeq platform. Its sequence shared 97.98% identity of the S. turicensis Type strain, and the ability of the Type strain to degrade cellulose was confirmed. Analysis of the genomic data focused on the cellulose operon. In addition to genes from the operon, we suggest that a gene following the operon may have an important role in regulating cellulose metabolism by signal transduction. This is the first report of S. turicensis found within microbiota of the animal gut. Because of its frequent presence in the kangaroo gut, we suggest that S. turicensis plays a role in cellulose digestion for kangaroos. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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16 pages, 2763 KiB

Open AccessArticle

Soybean Oil Modulates the Gut Microbiota Associated with Atherogenic Biomarkers

by Hila Korach-Rechtman, Oren Rom, Lirane Mazouz, Shay Freilich, Helana Jeries, Tony Hayek, Michael Aviram and Yechezkel Kashi

Microorganisms 2020, 8(4), 486; https://doi.org/10.3390/microorganisms8040486 - 30 Mar 2020

Cited by 9 | Viewed by 7767

Abstract

During the last few decades there has been a staggering rise in human consumption of soybean-oil (SO). The microbiome and specific taxa composing it are dramatically affected by diet; specifically, by high-fat diets. Increasing evidence indicates the association between dysbiosis and health or disease state, including cardiovascular diseases (CVD) and atherosclerosis pathogenesis in human and animal models. To investigate the effects of high SO intake, C57BL/6 mice were orally supplemented with SO-based emulsion (SOE) for one month, followed by analyses of atherosclerosis-related biomarkers and microbiota profiling by 16S rRNA gene sequencing of fecal DNA. SOE-supplementation caused compositional changes to 64 taxa, including enrichment in Bacteroidetes, Mucispirillum, Prevotella and Ruminococcus, and decreased Firmicutes. These changes were previously associated with atherosclerosis in numerous studies. Among the shifted taxa, 40 significantly correlated with at least one atherosclerosis-related biomarker (FDR < 0.05), while 13 taxa positively correlated with the average of all biomarkers. These microbial alterations also caused a microbial-derived metabolic-pathways shift, including enrichment in different amino-acid metabolic-pathways known to be implicated in CVD. In conclusion, our results demonstrate dysbiosis following SOE supplementation associated with atherosclerosis-related biomarkers. These findings point to the microbiome as a possible mediator to CVD, and it may be implemented into non-invasive diagnostic tools or as potential therapeutic strategies. Full article

(This article belongs to the Special Issue Animal Microbiota: Securing Optimal Gene-Diet-Microbiota Interactions)

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