scholarly journals Gut Microbial Divergence between Two Populations of the Hadal AmphipodHirondellea gigas

2018 ◽  
Vol 85 (1) ◽  
Author(s):  
Weipeng Zhang ◽  
Hiromi Kayama Watanabe ◽  
Wei Ding ◽  
Yi Lan ◽  
Ren-Mao Tian ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Taxonomic Composition ◽  
Microbial Interactions ◽  
Japan Trench ◽  
Microbial Composition ◽  
Mariana Trench ◽  
Content Type ◽  
Alpha And Beta Diversity ◽  
Functional Potential

ABSTRACTHadal environments sustain diverse microorganisms. A few studies have investigated hadal microbial communities consisting of free-living or particle-associated bacteria and archaea. However, animal-associated microbial communities in hadal environments remain largely unexplored, and comparative analyses of animal gut microbiota between two isolated hadal environments have never been done so far. In the present study, 228 Gb of gut metagenomes of the giant amphipodHirondellea gigasfrom two hadal trenches, the Mariana Trench and Japan Trench, were sequenced and analyzed. Taxonomic analysis identified 49 microbial genera commonly shared by the gut microbiota of the twoH. gigaspopulations. However, the results of statistical analysis, in congruency with the alpha and beta diversity analyses, revealed significant differences in gut microbial composition across the two trenches. Abundance variation ofPsychromonas,Propionibacterium, andPseudoalteromonasspecies was observed. Microbial cooccurrence was demonstrated for microbes that were overrepresented in the Mariana trench. Comparison of functional potential showed that the percentage of carbohydrate metabolic genes among the total microbial genes was significantly higher in the guts ofH. gigasspecimens from the Mariana Trench. Integrating carbon input information and geological characters of the two hadal trenches, we propose that the differences in the community structure might be due to several selective factors, such as environmental variations and microbial interactions.IMPORTANCEThe taxonomic composition and functional potential of animal gut microbiota in deep-sea environments remain largely unknown. Here, by performing comparative metagenomics, we suggest that the gut microbial compositions of twoHirondellea gigaspopulations from the Mariana Trench and the Japan Trench have undergone significant divergence. Through analyses of functional potentials and microbe-microbe correlations, our findings shed light on the contributions of animal gut microbiota to host adaptation to hadal environments.

scholarly journals New View on Dietary Fiber Selection for Predictable Shifts in Gut Microbiota

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
T. M. Cantu-Jungles ◽  
B. R. Hamaker
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Dietary Fiber ◽  
Physical Characteristics ◽  
Dietary Fibers ◽  
Human Gut ◽  
Microbial Composition ◽  
Human Gut Microbiota ◽  
Selection For ◽  
Fiber Selection

ABSTRACT Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate. The use of such fibers as prebiotics targeted to specific microbes would result in predictable shifts independent of the background microbial composition.

scholarly journals An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists

Life ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 185
Author(s):  
Hamza Mbareche ◽  
Nathan Dumont-Leblond ◽  
Guillaume J. Bilodeau ◽  
Caroline Duchaine
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Statistical Tests ◽  
Repeated Measurements ◽  
Microbial Composition ◽  
Alpha And Beta Diversity ◽  
Bioinformatic Tools ◽  
Bioinformatics Tools ◽  
Wide Range ◽  
Guided Tour

High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

scholarly journals Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Justinn Renelies-Hamilton ◽  
Kristjan Germer ◽  
David Sillam-Dussès ◽  
Kasun H. Bodawatta ◽  
Michael Poulsen
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Vertical Transmission ◽  
Priority Effects ◽  
Rrna Gene ◽  
Combined Effects ◽  
Microbial Composition ◽  
Host Fitness ◽  
Microbial Invasion ◽  
Host Taxon

ABSTRACT A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments. IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.

scholarly journals Covert Cross-Feeding Revealed by Genome-Wide Analysis of Fitness Determinants in a Synthetic Bacterial Mutualism

2020 ◽  
Vol 86 (13) ◽  
Author(s):  
Breah LaSarre ◽  
Adam M. Deutschbauer ◽  
Crystal E. Love ◽  
James B. McKinlay
Keyword(s):  
Escherichia Coli ◽  
Microbial Communities ◽  
Rhodopseudomonas Palustris ◽  
Microbial Interactions ◽  
Dependent Manner ◽  
Fermentation Products ◽  
Content Type ◽  
E Coli ◽  
Cellular Processes ◽  
Genome Wide

ABSTRACT Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairing Escherichia coli and Rhodopseudomonas palustris, wherein E. coli provides carbon to R. palustris in the form of glucose fermentation products and R. palustris fixes N2 gas and provides nitrogen to E. coli in the form of NH4+. The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search for E. coli genes that influence fitness during cooperative growth with R. palustris. RB-TnSeq revealed hundreds of genes that increased or decreased E. coli fitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. In addition, we discovered unexpected purine cross-feeding from R. palustris to E. coli, with coculture rescuing growth of an E. coli purine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictable a priori. IMPORTANCE Microbial communities impact life on Earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influenced Escherichia coli fitness during cooperative growth with a mutualistic partner, Rhodopseudomonas palustris. Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen, E. coli fitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.

scholarly journals Inclusion of Konjac Flour in the Gestation Diet Changes the Gut Microbiota, Alleviates Oxidative Stress, and Improves Insulin Sensitivity in Sows

2016 ◽  
Vol 82 (19) ◽  
pp. 5899-5909 ◽  
Author(s):  
Chengquan Tan ◽  
Hongkui Wei ◽  
Jiangtao Ao ◽  
Guang Long ◽  
Jian Peng
Keyword(s):  
Oxidative Stress ◽  
Insulin Sensitivity ◽  
Gut Microbiota ◽  
Control Diet ◽  
Rrna Gene ◽  
Model Assessment ◽  
Microbial Composition ◽  
Content Type ◽  
Konjac Flour ◽  
Host Metabolism

ABSTRACTAlthough dietary fibers contribute to health and physiology primarily via the fermentative actions of the gut microbiota of the hosts, few studies have focused on how these interactions influence the metabolic status of sows. Here, the effects of inclusion of konjac flour (KF) in a gestation diet on oxidative stress status, insulin sensitivity, and gut microbiota were investigated to elucidate the correlation between the microbiota and metabolic changes in sows. Sows were assigned to either control or 2.2% KF dietary treatment during gestation. The gut microbiota population in sows during gestation and lactation was assessed by 16S rRNA gene sequencing. The oxidative stress parameters, homeostasis model assessment (HOMA) values, and fatty acids in the blood of sows were also assessed. Compared to the control diet group, KF significantly reduced the serum levels of reactive oxygen species (ROS) and 8-hydroxy-deoxyguanosine (8-OHdG) but increased the serum concentrations of glutathione peroxidase (GSH-Px) in sows on day 1 in lactation. Additionally, sows in the KF group had a lower HOMA insulin resistance value but a higher HOMA insulin sensitivity (HOMA-IS) value. KF induced changes in the gut microbial composition at the phylum and genus levels. The increased relative abundances ofAkkermansiaandRoseburiain the KF group were positively correlated with the HOMA-IS. Overall, dietary KF alleviated oxidative stress and improved insulin sensitivity of sows, and the changes in the gut microbiota in response to KF may have been correlated with the host metabolism response.IMPORTANCETo date, the effect of dietary fiber on metabolism responses and gut microbiota in sows has not been investigated. Here, KF supplementation of a gestation diet in sows was found to alleviate oxidative stress and to improve insulin sensitivity. Pyrosequencing analysis revealed that KF treatment induces changes in the gut microbiota composition at the phylum and genus levels. Moreover, the changes of gut microbiota in response to KF may be correlated with the host metabolism response.

scholarly journals Genome Reduction inPsychromonasSpecies within the Gut of an Amphipod from the Ocean’s Deepest Point

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Weipeng Zhang ◽  
Ren-Mao Tian ◽  
Jin Sun ◽  
Salim Bougouffa ◽  
Wei Ding ◽  
...  
Keyword(s):  
Nutrient Utilization ◽  
Microbial Composition ◽  
Free Living ◽  
Carbohydrate Utilization ◽  
Mariana Trench ◽  
Associated Bacteria ◽  
Content Type ◽  
Genomic Analyses ◽  
And Function ◽  
Central Carbohydrate Metabolism

ABSTRACTAmphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth’s oceans. Here the gut microbiota of the amphipodHirondellea gigascollected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated byPsychromonas, of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-livingPsychromonasstrains, CDP1 has a highly reduced genome. Genome alignment showed deletion of the trimethylamineN-oxide (TMAO) reducing gene cluster in CDP1, suggesting that the “piezolyte” function of TMAO is more important than its function in respiration, which may lead to TMAO accumulation. In terms of nutrient utilization, the bacterium retains its central carbohydrate metabolism but lacks most of the extended carbohydrate utilization pathways, suggesting the confinement ofPsychromonasto the host gut and sequestration from more variable environmental conditions. Moreover, CDP1 contains a complete formate hydrogenlyase complex, which might be involved in energy production. The genomic analyses imply that CDP1 may have developed adaptive strategies for a lifestyle within the gut of the hadal amphipodH. gigas.IMPORTANCEAs a unique but poorly investigated habitat within marine ecosystems, hadal trenches have received interest in recent years. This study explores the gut microbial composition and function in hadal amphipods, which are among the dominant carrion feeders in hadal habitats. Further analyses of a dominant strain revealed genomic features that may contribute to its adaptation to the amphipod gut environment. Our findings provide new insights into animal-associated bacteria in the hadal biosphere.

scholarly journals Nutrient supplementation experiments on saltern microbial communities support utilization of DNA as a source of phosphorus

2020 ◽  
Author(s):  
Zhengshuang Hua ◽  
Matthew Ouellette ◽  
Andrea M. Makkay ◽  
R. Thane Papke ◽  
Olga Zhaxybayeva
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Inorganic Phosphorus ◽  
Taxonomic Composition ◽  
Community Response ◽  
Extracellular Dna ◽  
Microbial Composition ◽  
Carbon And Nitrogen ◽  
Phosphorus Source ◽  
Preferential Uptake

AbstractAll environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities could use DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. Additionally, microcosms’ composition shifted substantially depending on the provided nutrient combinations. These shifts allowed us to predict supplemented nutrients from microbial composition with high accuracy, suggesting that nutrient availability in an environment could be assessed from a taxonomic survey of its microbial community.

scholarly journals Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective

2021 ◽  
Vol 7 (8) ◽  
Author(s):  
Jacky Dwiyanto ◽  
Qasim Ayub ◽  
Sui Mae Lee ◽  
Su Chern Foo ◽  
Chun Wie Chong ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Ethnic Groups ◽  
Meta Analysis ◽  
Ethnic Origin ◽  
Rrna Gene ◽  
Analysis Model ◽  
Human Gut ◽  
Microbial Composition ◽  
Content Type ◽  
Geographical Separation

Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA R 2=0.005, pseudo-F=2.643, P=0.001). A sparse partial least squares – discriminant analysis model trained using the gut microbiota of individuals from China, India and Indonesia (representation of Chinese, Indian and Malay ethnic group, respectively) showed a better-than-random performance in classifying Malaysian of Chinese descent, although the performance for Indian and Malay were modest (true prediction rate, Chinese=0.60, Indian=0.49, Malay=0.44). Separately, differential abundance analysis singled out Ligilactobacillus as being elevated in Indians. We postulate that despite the strong influence of geographical factors on the gut microbiota, cultural similarity due to a shared ethnic origin drives the presence of a shared gut microbiota composition. The interplay of these factors will likely depend on the circumstances of particular groups of migrants.

scholarly journals Daily feeding rhythm linked to microbiome composition in two zooplankton species

2021 ◽  
Author(s):  
Alaina C Pfenning-Butterworth ◽  
Reilly Cooper ◽  
Clay Cressler
Keyword(s):  
Feeding Behavior ◽  
Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Daily Feeding ◽  
Microbiome Diversity ◽  
Rrna Sequencing ◽  
Host Phylogeny ◽  
Induced Changes

Host-associated microbial communities are impacted by external and within-host factors, i.e., diet and feeding behavior. For organisms known to have a circadian rhythm in feeding behavior, microbiome composition is likely impacted by the different rates of microbe introduction and removal across a daily cycle, in addition to any diet-induced changes in microbial interactions. Here, we measured feeding behavior and used 16S rRNA sequencing to compare the microbial community across a diel cycle in two distantly related species of Daphnia, that differ in their life history traits, to assess how daily feeding patterns impact microbiome composition. We find that Daphnia species reared under similar laboratory conditions have significantly different microbial communities. Additionally, we reveal that Daphnia have daily differences in their microbial composition that correspond with feeding behavior, such that there is greater microbiome diversity at night during the host's active feeding phase. These results highlight that zooplankton microbiomes are relatively distinct and are likely influenced by host phylogeny.

scholarly journals Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients

2016 ◽  
Vol 82 (22) ◽  
pp. 6633-6644 ◽  
Author(s):  
Francesco Paroni Sterbini ◽  
Alessandra Palladini ◽  
Luca Masucci ◽  
Carlo Vittorio Cannistraci ◽  
Roberta Pastorino ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Proton Pump Inhibitors ◽  
Proton Pump ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Content Type ◽  
Treatment Regimens ◽  
H Pylori ◽  
Content Status ◽  
Gastric Microbiota

ABSTRACTBesides being part of anti-Helicobacter pyloritreatment regimens, proton pump inhibitors (PPIs) are increasingly being used to treat dyspepsia. However, little is known about the effects of PPIs on the human gastric microbiota, especially those related toH. pyloriinfection. The goal of this study was to characterize the stomach microbial communities in patients with dyspepsia and to investigate their relationships with PPI use andH. pyloristatus. Using 16S rRNA gene pyrosequencing, we analyzed the mucosa-associated microbial populations of 24 patients, of whom 12 were treated with the PPI omeprazole and 9 (5 treated and 4 untreated) were positive forH. pyloriinfection. TheProteobacteria,Firmicutes,Bacteroidetes,Fusobacteria, andActinobacteriaphyla accounted for 98% of all of the sequences, withHelicobacter,Streptococcus, andPrevotellaranking among the 10 most abundant genera.H. pyloriinfection or PPI treatment did not significantly influence gastric microbial species composition in dyspeptic patients. Principal-coordinate analysis of weighted UniFrac distances in these communities revealed clear but significant separation according toH. pyloristatus only. However, in PPI-treated patients,Firmicutes, particularlyStreptococcaceae, were significantly increased in relative abundance compared to those in untreated patients. Consistently,Streptococcuswas also found to significantly increase in relation to PPI treatment, and this increase seemed to occur independently ofH. pyloriinfection. Our results suggest thatStreptococcusmay be a key indicator of PPI-induced gastric microbial composition changes in dyspeptic patients. Whether the gastric microbiota alteration contributes to dyspepsia needs further investigation.IMPORTANCEAlthough PPIs have become a popular treatment choice, a growing number of dyspeptic patients may be treated unnecessarily. We found that patients treated with omeprazole showed gastric microbial communities that were different from those of untreated patients. These differences regarded the abundances of specific taxa. By understanding the relationships between PPIs and members of the gastric microbiota, it will be possible to envisage new strategies for better managing patients with dyspepsia.

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