scholarly journals The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Pierre Legendre ◽  
Claude Guertin
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Strong Predictor ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Food Sources ◽  
Microbiome Composition ◽  
Living Organisms ◽  
Insect Gut ◽  
Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

scholarly journals Differences in Gut Microbiome Composition Between Sympatric Wild and Allopatric Laboratory Populations of Omnivorous Cockroaches

2021 ◽  
Vol 12 ◽  
Author(s):  
Kara A. Tinker ◽  
Elizabeth A. Ottesen
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Periplaneta Americana ◽  
Laboratory Environment ◽  
Microbiome Composition ◽  
Relative Contribution ◽  
Microbiome Diversity ◽  
Before And After ◽  
Laboratory Populations ◽  
Gut Microbial Community

Gut microbiome composition is determined by a complex interplay of host genetics, founder’s effects, and host environment. We are using omnivorous cockroaches as a model to disentangle the relative contribution of these factors. Cockroaches are a useful model for host–gut microbiome interactions due to their rich hindgut microbial community, omnivorous diet, and gregarious lifestyle. In this study, we used 16S rRNA sequencing to compare the gut microbial community of allopatric laboratory populations of Periplaneta americana as well as sympatric, wild-caught populations of P. americana and Periplaneta fuliginosa, before and after a 14 day period of acclimatization to a common laboratory environment. Our results showed that the gut microbiome of cockroaches differed by both species and rearing environment. The gut microbiome from the sympatric population of wild-captured cockroaches showed strong separation based on host species. Laboratory-reared and wild-captured cockroaches from the same species also exhibited distinct gut microbiome profiles. Each group of cockroaches had a unique signature of differentially abundant uncharacterized taxa still present after laboratory cultivation. Transition to the laboratory environment resulted in decreased microbiome diversity for both species of wild-caught insects. Interestingly, although laboratory cultivation resulted in similar losses of microbial diversity for both species, it did not cause the gut microbiome of those species to become substantially more similar. These results demonstrate how competing factors impact the gut microbiome and highlight the need for a greater understanding of host–microbiome interactions.

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

scholarly journals Food Starch Structure Impacts Gut Microbiome Composition

mSphere ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Frederick J. Warren ◽  
Naoki M. Fukuma ◽  
Deirdre Mikkelsen ◽  
Bernadine M. Flanagan ◽  
Barbara A. Williams ◽  
...  
Keyword(s):  
Small Intestine ◽  
Microbial Community ◽  
Gut Microbiome ◽  
Nutritive Value ◽  
Human Diet ◽  
Fermentation Products ◽  
Microbiome Composition ◽  
Starch Fermentation ◽  
Starch Structure

ABSTRACT Starch is a major source of energy in the human diet and is consumed in diverse forms. Resistant starch (RS) escapes small intestinal digestion and is fermented in the colon by the resident microbiota, with beneficial impacts on colonic function and host health, but the impacts of the micro- and nanoscale structure of different physical forms of food starch on the broader microbial community have not been described previously. Here, we use a porcine in vitro fermentation model to establish that starch structure dramatically impacts microbiome composition, including the key amylolytic species, and markedly alters both digestion kinetics and fermentation outcomes. We show that three characteristic food forms of starch that survive digestion in the small intestine each give rise to substantial and distinct changes in the microbiome and in fermentation products. Our results highlight the complexity of starch fermentation processes and indicate that not all forms of RS in foods are degraded or fermented in the same way. This work points the way for the design of RS with tailored degradation by defined microbial communities, informed by an understanding of how substrate structure influences the gut microbiome, to improve nutritive value and/or health benefits. IMPORTANCE Dietary starch is a major component in the human diet. A proportion of the starch in our diet escapes digestion in the small intestine and is fermented in the colon. In this study, we use a model of the colon, seeded with porcine feces, in which we investigate the fermentation of a variety of starches with structures typical of those found in foods. We show that the microbial community changes over time in our model colon are highly dependent on the structure of the substrate and how accessible the starch is to colonic microbes. These findings have important implications for how we classify starches reaching the colon and for the design of foods with improved nutritional properties.

scholarly journals Dietary sphinganine is selectively assimilated by members of the gut microbiome

2020 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H. Le ◽  
Elizabeth L. Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Bioactive Components ◽  
Microbiome Composition ◽  
Metabolic Products ◽  
Comparative Metabolomics ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

scholarly journals Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas

2017 ◽  
Vol 284 (1862) ◽  
pp. 20170955 ◽  
Author(s):  
Qi Wu ◽  
Xiao Wang ◽  
Yun Ding ◽  
Yibo Hu ◽  
Yonggang Nie ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Cell Cycle Control ◽  
Nutrient Utilization ◽  
Giant Pandas ◽  
Microbiome Composition ◽  
Leaf Stage ◽  
Bamboo Shoots ◽  
And Function ◽  
Gut Microbial Community ◽  
Metagenomic Approach

Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different. Functional metagenomic analysis showed that in the leaf stage, bacteria species over-represented genes involved in raw fibre utilization and cell cycle control. Thus, raw fibre utilization by the gut microbiome was guaranteed during the nutrient-deficient leaf stage by reinforcing gut microbiome robustness. During the protein-abundant shoot stage, the functional capacity of the gut microbiome expanded to include prokaryotic secretion and signal transduction activity, suggesting active interactions between the gut microbiome and host. These results illustrate that seasonal nutrient variation in wild giant pandas substantially influences gut microbiome composition and function. Nutritional interactions between gut microbiomes and hosts appear to be complex and further work is needed.

scholarly journals Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

2020 ◽  
pp. jlr.RA120000950 ◽  
Author(s):  
Min-Ting Lee ◽  
Henry H Le ◽  
Elizabeth L Johnson
Keyword(s):  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Dietary Lipids ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Bioorthogonal Labeling ◽  
Comparative Metabolomics ◽  
Metabolic Activities ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

scholarly journals Host Habitat Is the Major Determinant of the Gut Microbiome of Fish

2021 ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Jae-Bong Lee ◽  
Min-Soo Kim ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Microbial Community Composition ◽  
Terrestrial Vertebrates ◽  
Symbiotic Relationships ◽  
Machine Learning Approach ◽  
Host Habitat ◽  
Functional Profiles ◽  
Gut Microbial Community

Abstract Background: Our understanding of the gut microbiota of animals is largely based on studies of mammals. To better understand the evolutionary basis of symbiotic relationships between animal hosts and indigenous microbes, it is necessary to investigate the gut microbiota of non-mammalian vertebrate species. In particular, fish have the highest species diversity among groups of vertebrates, with approximately 33,000 species. In this study, we comprehensively characterized gut bacterial communities in fish.Results: We analyzed 227 individual fish representing 14 orders, 42 families, 79 genera, and 85 species. The fish gut microbiota was dominated by Proteobacteria (51.7%) and Firmicutes (13.5%), different from the dominant taxa reported in terrestrial vertebrates (Firmicutes and Bacteroidetes). The gut microbial community in fish was more strongly shaped by host habitat than by host taxonomy or trophic level. Using a machine learning approach trained on the microbial community composition or predicted functional profiles, we found that the host habitat exhibited the highest classification accuracy. Principal coordinate analysis revealed that the gut bacterial community of fish differs significantly from those of other vertebrate classes (reptiles, birds, and mammals).Conclusions: Collectively, these data provide a reference for future studies of the gut microbiome of aquatic animals as well as insights into the relationship between fish and their gut bacteria, including the key role of host habitat and the distinct compositions in comparison with those of mammals, reptiles, and birds.

scholarly journals Bacteriophages in Gut Microbiome Interactions in Patients with Inflammatory Bowel Disease: Differences by Sex and The Disease Type

2022 ◽  
Author(s):  
Fatemeh Farahmandzad ◽  
Hossein Lanjanian ◽  
Ehsan Arefian ◽  
Kaveh Kavousi
Keyword(s):  
Ulcerative Colitis ◽  
Inflammatory Bowel Disease ◽  
Crohn’S Disease ◽  
Microbial Community ◽  
Crohn's Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Disease Type ◽  
Inflammatory Bowel ◽  
Gut Microbial Community

Abstract Background: Inflammatory bowel disease (IBD), known as the disease of the century, is a complex condition that affects millions of people worldwide. IBD is influenced by numerous factors such as genetics, lifestyle, and the gut microbial community, yet the role of microorganisms in driving and controlling the disease remains poorly understood. As we know, preceding studies have mainly focused on assessing gut bacteria and less on bacteriophages or fungi, and no study on interactions of the gut microbial community in patients with IBD has looked at bacteriophages in addition to bacteria and fungi by sex. No distinct microbial regulatory candidate has been proposed so far.Results: Here, metagenomic data were obtained from 456 stool samples of 84 white race volunteers (40 females and 44 males) with no treatment history before sampling. Participants were studied by sex and the disease type using bioinformatics methods. Differences in interactions of bacteriophages, bacteria, fungi, and archaea in the gut of males and females with Crohn's disease were remarkable, indicating the necessity for different therapies for both groups. While, little difference was seen in the gut microbiome relations in females and males with ulcerative colitis.Conclusions: The fungal strain Malassezia globose CBS 7966 beside the bacterial species Bacteroides stercorisin ulcerative colitis and Parabacteroides phage YZ-2015b in Crohn's disease were the sex-independent regulatory candidates. Uncultured crAssphage was recommended as a sex-dependent regulatory candidate for IBD in men. However, the fungus Wickerhamomycesciferrii which had proposed as regulatory candidate in Crohn's disease, was age-dependent in females. Four bacteriophages, such as Escherichia phage pro147, were suggested for study candidates in the metabolism of IBD.

Understanding the development of the gut microbiome in pigs: an overview

2022 ◽  
pp. 179-202
Author(s):  
Marion Borey ◽  
◽  
Jordi Estelle ◽  
Claire Rogel-Gaillard ◽  
◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Environmental Changes ◽  
Feed Additives ◽  
Fecal Microbiome ◽  
Host Genetics ◽  
Microbiome Composition ◽  
Living Organisms ◽  
Host Development

Living organisms continuously and intimately interact with commensal microbial communities referred to as microbiota and microbiomes. These complex ecosystems provide their hosts with vital services. The gut microbiome develops and diversifies after birth in pigs, as in all mammals. The diversification dynamics follows the host development early in life, reaches an initial level of richness and stabilization before 60 days of age, and continues to mature but at a much lower rate while ageing and adapting to environmental changes. There is a wide variation in microbiome composition at individual and group levels, due to a combination of many factors including host genetics, environmental factors, feed and feed additives, and farm practices. Although the gut microbiome displays region-specific composition along the digestive tract, with likely sequential, complementary biological functionalities, the fecal microbiome is often considered as a good surrogate and provides many of the associations identified with host phenotypes.

scholarly journals Succession of the Gut Microbiome in the Tibetan Population of Minjiang River Basin

2020 ◽  
Author(s):  
Jun Li ◽  
Lin Sun ◽  
Chunfeng Mo ◽  
Xiangsheng Fu ◽  
Baijun Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Altitude ◽  
River Basin ◽  
Gut Microbiome ◽  
Tibet Plateau ◽  
Gut Microflora ◽  
Microbial Composition ◽  
Tibetan Population ◽  
Minjiang River ◽  
Gut Microbial Community

Abstract Background: Tibetans are one of the oldest ethnic groups in China and South Asia. Tibetan has a unique lifestyle and a long history, which leads to the particularity of their gut microflora in composition and function. Different from the Tibetan population on the Qinghai-Tibet Plateau, Tibetans in Minjiang River Basin have gradually increased their migration to Chengdu Plain in recent years. Based on the analysis of 1059 Tibetans in the Minjiang River Basin at an altitude of 500-4001m, we found that the dominant phylum of Tibetan population is Bacteroidea and Firmicum, and the main genera are Prevotella and Bacteroides. These findings reflect the characteristics of Tibetan population. Results: In order to further study the factors affecting gut microbial composition of Tibetan population, 115 total parameters of 7 categories were evaluated. The results showed that altitude was the most important factor affecting the variation of microbial community in Tibetan population, and the change of altitude promoted the succession of gut microbial community. In the process of migration from high altitude to plain, the intestinal microbial composition of late immigrants was similar to that of plateau aborigines, while that of early immigrants was similar to that of plain aborigines. Migration to Tibet is related to the loss of indigenous gut microbial community species. In addition, from low altitude to high altitude, the similarity of microbial community with high altitude population increased with the reproduction of offspring after marriage. And the change of these flora will affect the metabolism, disease and cell function of Tibetan population. The other two sets (AGP and Z208) of altitude data also show the impact of altitude on the microbial community. Conclusions: This is the first large-scale study on the influencing factors of gut microflora in Tibetan population. Our study confirmed that altitude change is the most important factor affecting the distribution of Tibetan population flora, and provided abundant and unique data to explore the interaction of impact parameter-gut microbiome-host function and disease.

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