scholarly journals The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere

2019 ◽  
Author(s):  
Talia L. Karasov ◽  
Manuela Neumann ◽  
Alejandra Duque-Jaramillo ◽  
Sonja Kersten ◽  
Ilja Bezrukov ◽  
...  
Keyword(s):  
Microbial Population ◽  
Taxonomic Composition ◽  
Plant Genome ◽  
Wild Plants ◽  
Shotgun Metagenomics ◽  
Microbial Cells ◽  
Plant Leaf ◽  
Microbiome Composition ◽  
Microbial Dysbiosis ◽  
Order Of Magnitude

AbstractA central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial population sizes. In addition to the number of microbial cells, information on taxonomic composition can provide important insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial cells often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.

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.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

2019 ◽  
Author(s):  
H. Soon Gweon ◽  
Liam P. Shaw ◽  
Jeremy Swann ◽  
Nicola De Maio ◽  
Manal AbuOun ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Open Source Software ◽  
River Sediment ◽  
Taxonomic Composition ◽  
Sequencing Depth ◽  
Gene Content ◽  
Metagenomic Data ◽  
Software Pipeline ◽  
Shotgun Metagenomics

ABSTRACTBackgroundShotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (∼200 million reads per sample). Alongside this, we cultured single-colony isolates ofEnterobacteriaceaefrom the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’.ResultsTaxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve <1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike ofThermus thermophilusDNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment.ConclusionsSequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

scholarly journals Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

2021 ◽  
Author(s):  
E. D. Baranova ◽  
V. G. Druzhinin ◽  
L. V. Matskova ◽  
P. S. Demenkov ◽  
V. P . Volobaev ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Inflammatory Responses ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cell Lung Carcinoma ◽  
Microbiome Composition ◽  
Β Diversity ◽  
Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

scholarly journals Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
T. Goolam Mahomed ◽  
R. P. H. Peters ◽  
M. Allam ◽  
A. Ismail ◽  
S. Mtshali ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Small Sample ◽  
Chronic Obstructive ◽  
Shotgun Metagenomics ◽  
Alpha And Beta Diversity ◽  
Microbiome Composition ◽  
Disease States ◽  
Dna And Rna ◽  
Lung Microbiome ◽  
Copd Patients

AbstractChronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.

scholarly journals Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Ganesh Babu Malli Mohan ◽  
Ceth W. Parker ◽  
Camilla Urbaniak ◽  
Nitin K. Singh ◽  
Anthony Hood ◽  
...  
Keyword(s):  
16S Rrna ◽  
Metal Surfaces ◽  
Microbial Population ◽  
Microbial Populations ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Particle Board ◽  
Shotgun Metagenomics ◽  
Glass Surfaces ◽  
Glass Metal

ABSTRACT Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance. IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.

The impact of human-facilitated selection on the gut microbiota of domesticated mammals

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
Giulia Alessandri ◽  
Christian Milani ◽  
Leonardo Mancabelli ◽  
Marta Mangifesta ◽  
Gabriele Andrea Lugli ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Horizontal Transmission ◽  
Taxonomic Composition ◽  
Functional Adaptation ◽  
Rrna Gene ◽  
Feed Conversion ◽  
Shotgun Metagenomics ◽  
Domesticated Animals ◽  
And Behavior ◽  
The Impact

ABSTRACT Domestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated–feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.

scholarly journals The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
H. Soon Gweon ◽  
◽  
Liam P. Shaw ◽  
Jeremy Swann ◽  
Nicola De Maio ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Open Source Software ◽  
River Sediment ◽  
Taxonomic Composition ◽  
Sequencing Depth ◽  
Gene Content ◽  
Metagenomic Data ◽  
Software Pipeline ◽  
Shotgun Metagenomics

Abstract Background Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’. Results Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment. Conclusions Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

scholarly journals Heliconius Butterflies Host Characteristic and Phylogenetically Structured Adult-Stage Microbiomes

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Tobin J. Hammer ◽  
Jacob C. Dickerson ◽  
W. Owen McMillan ◽  
Noah Fierer
Keyword(s):  
Bacterial Communities ◽  
Evolutionary Biology ◽  
Adult Stage ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phylogenetic Structure ◽  
Shotgun Metagenomics ◽  
Microbiome Composition ◽  
Form And Function ◽  
Passion Vine

ABSTRACT Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from those of microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius butterflies harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of the host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that the phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and colocalized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology. IMPORTANCE Many insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear because in many insect taxa, microbiomes have been studied in only part of the life cycle, if at all. A prominent example is butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius. Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and insect-microbe interactions generally.

scholarly journals Characterizing the Gut Microbiome of Dietary Patterns Using Pooled Samples: Assessing a Novel Methodological Approach to a Complex Web of Confounders

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 1157-1157
Author(s):  
Leigh Frame ◽  
Stephanie Servetas ◽  
Scott Jackson
Keyword(s):  
Dietary Patterns ◽  
Dietary Pattern ◽  
Methodological Approach ◽  
Evidence Base ◽  
Shotgun Metagenomics ◽  
Microbiome Composition ◽  
Funding Sources ◽  
Metabolomic Data ◽  
The Individual ◽  
Pooled Samples

Abstract Objectives The response to a dietary pattern exhibits large interindividual variability—due in part to the uniqueness of the microbiome of each individual. However, specific attributes of the microbiome related to dietary intake may be directly related to the precise dietary pattern. To determine what attributes come solely from a dietary pattern, we must isolate the individual differences. To do this, we aim to establish the feasibility of assessing microbiome attributes related to disparate dietary patterns using pooled samples. Methods Samples from 4 self-identified vegans and omnivores were collected, pooled, homogenized and stored at −80°C until time of analysis. Dietary patterns were self-reported using DietID. Whole genome shotgun metagenomics was performed (Replicates: 10/diet, 4/individual). Metabolomic profiles were analyzed using NMR and MS/MS. Genomic and metabolomic data were analyzed to identify diet-specific signatures. As part of a comprehensive literature review, we developed a table predictive of the microbiomes of omnivores versus vegans. We compare our findings to this summary of emerging research to assess potential validity of pooled sample analysis. Results Key differences were detected between the vegan and omnivore samples individually and in pools including 10 genera significantly enriched in vegan and 15 in omnivore, e.g., Akkermansia, Bacteroides, Bifidobacterium, Clostridium, Faecalibacterium, Methanobrevibacter, and Ruminococcus. Fold changes were &gt; 2 in 13 of 25 genera (4 vegan, 9 omnivore). Differences were comparable to the predictive table. Ongoing analyses include comparisons at additional taxonomic levels and diversity/richness assessments which will improve the resolution of the aforementioned relationships and the ability to detect them using pooled samples. Conclusions Even with a small cohort of pooled samples, we are able to reproduce the findings of the evidence-base to-date—the same variability and stability in microbiome composition. Funding Sources National Institute of Standards and Technology (NIST), The International Life Sciences Institute – North America (ILSI-NA).

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