Undaria pinnatifida Intake Rapidly Affects the Gut Microbiome Community: A Controlled Feeding Trial

Abstract Objectives The gut microbiome is closely related to health and influenced by dietary intake. However, little is known how seaweed, a food high in fiber, affects the gut microbiome. We investigated the effect of sea mustard (Undaria pinnatifida), a commonly consumed seaweed in East Asia, on the gut microbial community. Methods Forty-two healthy women aged 40–65 years participated as the ocean group (n = 22) or city control (n = 20; CC) for 20 days. The ocean group was housed on an island and participated in a 5-day program of mind-body exercises and controlled-feeding before returning to one's daily routine. Within the ocean group, participants were randomly assigned to control (OC) or to additionally consume sea mustard (OS; 15.4 g dry weight/d; n = 11/group). Sea mustard was provided in various dishes to the OS group during the 5-day program on the island where food intake and activity participation were controlled and monitored. Sea mustard noodles were provided to OS participants to consume during the following two weeks. CC did not receive any intervention. Groups OC and OS collected feces on days 0, 5 (before leaving the island), and 20. CC collected 3 fecal samples within a 20-day period. Fecal samples were sequenced for bacterial 16S rRNA. Analyses were performed by ANOVA, mixed ANOVA, and paired t-test. Results Alpha and β-diversity did not differ between groups at baseline. A time and group interaction was found for α-diversity. Among the top 30 abundant taxa, the only change in the CC group was the decrease in Roseburia by day 20. Lactococcus, Eubacterium_ventrioum_group, Ruminococcaceae_UCG005, and Bifidobacterium increased by day 5 in both OC and OS. The increase in Blautia and decrease in Prevotella observed in OC during the 5-day controlled-feeding period was not found in OS. Specific to OS, Bacteroides increased and Anaerostipes and Catenibacterium decreased by day 5. The abundance of Lachnospiraceae_NK4A136_group was increased throughout the 20-day sea mustard intervention in OS. Conclusions Change in environment can affect the gut microbial community even within 5 days. Sea mustard intake affects α-diversity of the gut microbiome and increases the abundance of Lachnospiraceae_NK4A136_group while preventing the decrease in Prevotella. Funding Sources The Ministry of Oceans and Fisheries, Korea.

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

Scientific Reports ◽

10.1038/s41598-021-95146-9 ◽

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.

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Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources

Animals ◽

10.3390/ani11061718 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1718

Author(s):

Kelang Kang ◽

Yan Hu ◽

Shu Wu ◽

Shourong Shi

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Fecal Microbiota ◽

Metagenomic Analysis ◽

Fecal Samples ◽

Microbial Community Function ◽

Community Function ◽

Rectal Swabs ◽

Gut Microbial Community

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.703785 ◽

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.

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

10.21203/rs.3.rs-332643/v1 ◽

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.

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

10.21203/rs.3.rs-1240997/v1 ◽

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.

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

10.21203/rs.3.rs-129100/v1 ◽

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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Gut microbiome to predict efficacy and immune-related toxicities in patients with advanced non-small cell lung cancer treated with anti-PD-1/PD-L1 antibody-based immunotherapy.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.3095 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 3095-3095

Author(s):

Taiki Hakozaki ◽

Corentin Richard ◽

Yusuke Okuma ◽

Lisa Derosa ◽

Arielle Elkrief ◽

...

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Clinical Outcomes ◽

Clinical Data ◽

Cell Lung Cancer ◽

Gut Microbiome ◽

Small Cell ◽

Small Cell Lung ◽

Fecal Samples ◽

Α Diversity

3095 Background: The gut microbiome (GM) plays an important role in shaping systemic immune responses. Preclinical and clinical data suggest that GM influences anti-PD-1/PD-L1 or -CTLA-4 Antibody (Ab)-mediated anti-cancer responses. Furthermore, there is strong evidence that antibiotics (ATB) worsen clinical outcomes based on multiple retrospective and one prospective studies using immune checkpoint inhibitor (ICI). However, whether GM profiling, at baseline or post-ATB, could represent a biomarker of response in advanced non-small cell lung cancer (NSCLC) during ICI therapy remains unknown. Methods: We prospectively collected baseline (pre-ICI) fecal samples and clinical data Japanese patients (pts) with NSCLC treated with anti-PD-1/PD-L1 Abs in first or second-line therapy. We performed a 16S rRNA V3-V4 sequencing of gene amplicons of fecal microbes. Amplicon sequence variants were generated with dada2 R package. Diversity analysis was performed with phyloseq R. Differential abundance analysis was performed with both LEfSe and DESeq2 methods. Clinical endpoints were progression-free survival (PFS), overall survival (OS), objective response rate (ORR), and immune-related adverse events (irAE). Results: 70 fecal samples were analyzed. Median OS and PFS in all patients were 16.1 and 5.2 months, respectively. 16 pts (23%) were exposed to ATB 1 month prior to ICI initiation. Pts on ATB had lower α-diversity at baseline and underrepresentation of Clostridiales and Ruminococcaceae UCG 13. When analyzing ATB-free pts, lower α-diversity was observed in non-responders. In addition, Ruminococcaceae UCG 13 was enriched in patients with OS > 12 months, favorable ORR, and PFS > 6 months. Clostridiales order was also enriched in patients with OS > 12 months. Compositional GM differences were also observed between the patients who experienced clinically significant (≥grade 2) irAE; Lactobacillaceae and Raoultella were enriched in pts who had no significant irAE. Conclusions: We demonstrated the negative influence of ATB on GM composition and identified differential bacteria repertoire in pts experiencing favorable clinical outcomes or low grade irAE. Our data pave the way to the development of diagnosis tools aimed at identifying gut dysbiosis to predict resistance or irAE during ICI for NSCLC.

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The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure

Genes ◽

10.3390/genes12010070 ◽

2021 ◽

Vol 12 (1) ◽

pp. 70

Author(s):

Lore Bulteel ◽

Shira Houwenhuyse ◽

Steven A. J. Declerck ◽

Ellen Decaestecker

Keyword(s):

Microbial Community ◽

Daphnia Magna ◽

Gut Microbiome ◽

Community Treatment ◽

Control Treatment ◽

Transplant Experiment ◽

Host Genotype ◽

Microbial Composition ◽

Gut Microbial Community

Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.

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Host habitat is the major determinant of the gut microbiome of fish

Microbiome ◽

10.1186/s40168-021-01113-x ◽

2021 ◽

Vol 9 (1) ◽

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.

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The gut microbiome as a driver of individual variation in cognition and functional behaviour

10.31219/osf.io/6gv9h ◽

2018 ◽

Author(s):

Gabrielle L Davidson ◽

Amy C. Cooke ◽

Crystal N. Johnson ◽

John L. Quinn

Keyword(s):

Microbial Community ◽

Brain Development ◽

Individual Variation ◽

Gut Microbiome ◽

Natural Populations ◽

Experimental Manipulation ◽

Animal Populations ◽

Microbiome Research ◽

And Function ◽

Gut Microbial Community

Research into proximate and ultimate mechanisms of individual cognitive variation in animal populations is a rapidly growing field that incorporates physiological, behavioural and evolutionary investigations. Recent studies in humans and lab animals have shown that the enteric microbial community plays a central role in brain development and functioning. The ‘gut-brain axis’ represents a multi-directional signalling system that encompasses neurological, immunological and hormonal pathways. In particular it is tightly linked with the hypothalamic-pituitary-adrenal axis (HPA), a system that regulates stress hormone release, and influences brain development and function. Experimental examination of the microbiome through manipulation of diet, infection, stress and exercise, suggests direct effects on cognition, including learning and memory. However, our understanding of these processes in natural populations is extremely limited. Here we outline how recent advances in predominantly laboratory-based microbiome research can be applied to understanding individual differences in cognition. Experimental manipulation of the microbiome across natal and adult environments will help to unravel the interplay between cognitive variation and the gut microbial community. Focus on individual variation in the gut microbiome and cognition in natural populations will reveal new insight into the environmental and evolutionary constraints that drive individual cognitive variation.

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