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.

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 Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 726
Author(s):  
Ronald Biemann ◽  
Enrico Buß ◽  
Dirk Benndorf ◽  
Theresa Lehmann ◽  
Kay Schallert ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Weight Loss ◽  
Gut Microbiome ◽  
Taxonomic Composition ◽  
Low Grade ◽  
Gut Inflammation ◽  
Functional Changes ◽  
Microbiome Composition ◽  
Before And After ◽  
Human Proteins

Gut microbiota-mediated inflammation promotes obesity-associated low-grade inflammation, which represents a hallmark of metabolic syndrome. To investigate if lifestyle-induced weight loss (WL) may modulate the gut microbiome composition and its interaction with the host on a functional level, we analyzed the fecal metaproteome of 33 individuals with metabolic syndrome in a longitudinal study before and after lifestyle-induced WL in a well-defined cohort. The 6-month WL intervention resulted in reduced BMI (−13.7%), improved insulin sensitivity (HOMA-IR, −46.1%), and reduced levels of circulating hsCRP (−39.9%), indicating metabolic syndrome reversal. The metaprotein spectra revealed a decrease of human proteins associated with gut inflammation. Taxonomic analysis revealed only minor changes in the bacterial composition with an increase of the families Desulfovibrionaceae, Leptospiraceae, Syntrophomonadaceae, Thermotogaceae and Verrucomicrobiaceae. Yet we detected an increased abundance of microbial metaprotein spectra that suggest an enhanced hydrolysis of complex carbohydrates. Hence, lifestyle-induced WL was associated with reduced gut inflammation and functional changes of human and microbial enzymes for carbohydrate hydrolysis while the taxonomic composition of the gut microbiome remained almost stable. The metaproteomics workflow has proven to be a suitable method for monitoring inflammatory changes in the fecal metaproteome.

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 0135 Self-Reported Sleep and Gut Microbiome Composition and Diversity: Associations in Well-Functioning Older Adults

SLEEP ◽  
2020 ◽  
Vol 43 (Supplement_1) ◽  
pp. A53-A53
Author(s):  
C Holingue ◽  
N T Mueller ◽  
T Tanaka ◽  
M K Differding ◽  
C W Chia ◽  
...  
Keyword(s):  
Older Adults ◽  
Sleep Duration ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Rating Scale ◽  
Self Report ◽  
Microbiome Composition ◽  
Microbiome Diversity ◽  
Falling Asleep ◽  
Insomnia Symptoms

Abstract Introduction The gut microbiome is believed to play an important role in health and disease, yet little is known about the link between sleep and the gut microbiome in humans. We investigated the association of self-reported sleep with gut microbiome composition and diversity in a cohort of well-functioning older adults. Methods We studied 791 participants (mean age = 71.5±12.0 years, 55% women) in the Baltimore Longitudinal Study of Aging with self-report sleep measures and whole-genome DNA sequencing of stool samples. Predictors (modeled as continuous variables) included insomnia symptoms from the Women’s Health Initiative Insomnia Rating Scale (WHIIRS), sleep duration (<5, 5–6, 6–7, >7 hours), and frequency of excessive daytime sleepiness (EDS). We tested their association with gut microbiome diversity (Shannon index) and relative abundance of individual taxa using Kendall Tau Correlation. Next, we assessed whether these sleep variables were associated with overall microbiome structure (Bray-Curtis), adjusting for age, sex, race, education, BMI, depressive symptoms, and number of comorbidities. Results Sleep duration was associated with overall microbiome composition (p<0.01), with longer sleep duration associated with lower biodiversity of microbes in the gut (p<0.05). In phylum-level analyses, higher WHIIRS total (i.e., more severe insomnia) was associated with lower relative abundance of Actinobacteria, while more frequent EDS was associated with lower relative abundance of Fusobacteria. More frequent trouble falling asleep, staying asleep, early waking, poorer sleep quality and higher WHIIRS total were associated with lower abundance of Synergistetes (all p<0.05). Conclusion In well-functioning older adults, self-reported sleep duration, symptoms of insomnia, and EDS were associated with microbiome diversity and composition. The phylum Synergistetes, which has been associated with protective humoral immune response in prior literature, may be an important correlate of insomnia symptoms in older adults. Future investigations are needed to examine the gut microbiome as a driver or mediator of sleep-health associations. Support This study was supported in part by National Institute on Aging (NIA) grant R01AG050507, the NIA Intramural Research Program (IRP), and Research and Development Contract HHSN-260-2004-00012C.

scholarly journals Lessons on dietary biomarkers from twin studies

2017 ◽  
Vol 76 (3) ◽  
pp. 303-307 ◽  
Author(s):  
Cristina Menni
Keyword(s):  
Gut Microbiome ◽  
Twin Studies ◽  
Dietary Interventions ◽  
Twin Design ◽  
Dietary Biomarkers ◽  
Microbiome Composition ◽  
Twin Model ◽  
Nutrition Research ◽  
Gene Environment ◽  
Microbiome Diversity

Metabolomic and microbiome profiling are promising tools to identify biomarkers of food intake and health status. The individual's genetic makeup plays a significant role on health, metabolism, gut microbes and diet and twin studies provide unique opportunities to untangle gene–environment effects on complex phenotypes. This brief review discusses the value of twin studies in nutrition research with a particular focus on metabolomics and the gut microbiome. Although, the twin model is a powerful tool to segregate the genetic component, to date, very few studies combine the twin design and metabolomics/microbiome in nutritional sciences. Moreover, since the individual's diet has a strong influence on the microbiome composition and the gut microbiome is modifiable (60 % of microbiome diversity is due to the environment), future studies should target the microbiome via dietary interventions.

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 Quantifying the impact of Human Leukocyte Antigen on the human gut microbiome

2020 ◽  
Author(s):  
Stijn P. Andeweg ◽  
Can Keşmir ◽  
Bas E. Dutilh
Keyword(s):  
Immune System ◽  
Gut Microbiome ◽  
Human Leukocyte ◽  
Human Gut ◽  
Microbiome Composition ◽  
Leukocyte Antigen ◽  
Human Gut Microbiome ◽  
Microbiome Diversity ◽  
Human Immune ◽  
Hla Molecules

AbstractObjectiveThe gut microbiome is affected by a number of factors, including the innate and adaptive immune system. The major histocompatibility complex (MHC), or the human leukocyte antigen (HLA) in humans, performs an essential role in vertebrate immunity, and is very polymorphic in different populations. HLA determines the specificity of T lymphocyte and natural killer (NK) cell responses, including against the commensal bacteria present in the human gut. Thus, it is likely that our HLA molecules and thereby the adaptive immune response, can shape the composition of our microbiome. Here, we investigated the effect of HLA haplotype on the microbiome composition.ResultsWe performed HLA typing and microbiota composition analyses on 3,002 public human gut microbiome datasets. We found that (i) individuals with functionally similar HLA molecules (i.e. presenting similar peptides) are also similar in their microbiota, and (ii) HLA homozygosity correlated with microbiome diversity, suggesting that diverse immune responses limit microbiome diversity.ConclusionOur results show a statistical association between host HLA haplotype and gut microbiome composition. Because the HLA haplotype is a readily measurable parameter of the human immune system, these results open the door to incorporating the immune system into predictive microbiome models.IMPORTANCEThe microorganisms that live in the digestive tracts of humans, known as the gut microbiome, are essential for hosts survival as they support crucial functions. For example, they support the host in facilitating the uptake of nutrients and give colonization resistance against pathogens. The composition of the gut microbiome varies among humans. Studies have proposed multiple factors driving the observed variation, including; diet, lifestyle, and health condition. Another major influence on the microbiome is the host’s genetic background. We hypothesized the immune system to be one of the most important genetic factors driving the differences observed between gut microbiomes. Therefore, we are interested in linking the polymorphic molecules that play a role in human immune responses to the composition of the microbiome. HLA molecules are the most polymorphic molecules in our genome and therefore makes an excellent candidate to test such an association/link. To our knowledge for the first time, our results indicate a significant impact of the HLA on the human gut microbiome composition.

scholarly journals Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes

2021 ◽  
Vol 12 ◽  
Author(s):  
Laila Silamiķele ◽  
Ivars Silamiķelis ◽  
Monta Ustinova ◽  
Zane Kalniņa ◽  
Ilze Elbere ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Gut Microbiome ◽  
High Fat Diet ◽  
Abundant Species ◽  
Metformin Treatment ◽  
High Fat ◽  
Microbiome Composition ◽  
Before And After ◽  
Diabetes Mouse

Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mouse models, depending on sex and metabolic status in well controlled experimental setting. Our study aimed to examine metformin-induced alterations in gut microbiome diversity, composition, and functional implications of high-fat diet-induced type 2 diabetes mouse model, using, for the first time in mice study, the shotgun metagenomic sequencing that allows estimation of microorganisms at species level. We also employed a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups to systematically evaluate the effect of sex and metabolic status on metformin interaction with microbiome. We used DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species relative abundances increased. In contrast, no significant changes were observed in control diet-fed mice. Functional analysis targeted to carbohydrate, lipid, and amino acid metabolism pathways revealed 14 significantly altered hierarchies. We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while in females the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. The same pattern manifested regarding the functional analysis, where we discovered 5 significantly affected hierarchies in female groups but not in males. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.

MICROBIOME DIVERSITY IN THE SALIVA RELATED ORAL AND SYSTEMIC DISEASES

2021 ◽  
pp. 3961-3973
Keyword(s):  
Microbial Community ◽  
Viral Infections ◽  
Modern Method ◽  
Health Condition ◽  
Metagenomic Analysis ◽  
Personal Health ◽  
Systemic Diseases ◽  
Analysis Method ◽  
Microbiome Composition ◽  
Microbiome Diversity

This review aimed to evaluate findings related to the human normal salivary microbiomes, the presence of opportunist salivary microbiome concerning oral and systemic diseases, and the use of salivary microbiome metagenomic analysis. Method: This review accomplishes using PubMed, Science Direct, and Google scholar. After reading the titles and abstracts, 2.718 works of literature screens for this review, content analysis performs. Results: Human normal salivary microbiomes consist of yeast, gram-positive, and gramnegative bacteria. A commensal microbial community founds in healthy people. An opportunist microbial community establishes in unhealthy people. It is essential to note an association between the opportunist microbiome composition with the personal health condition. Specific opportunist microbiome relates to particular diseases, such as diabetes, respiratory diseases, cancer, autoimmune, and viral infections. Even is different results of the conventional method and the modern methods (metagenomic analysis), both approaches can determine the presence of specific opportunist salivary microbiome concerning certain systemic diseases. Conclusion: Salivary microbiome composition can be a biomarker for people's health conditions and various systemic diseases. Both conventional methods and the modern method can be used complementarily for biomarker determination.

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.

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