scholarly journals The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria J. Soto-Giron ◽  
Ji-Nu Kim ◽  
Eric Schott ◽  
Claudine Tahmin ◽  
Thomas Ishoey ◽  
...  
Keyword(s):  
Fruits And Vegetables ◽  
Growth Promotion ◽  
Functional Characterization ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Plant Host ◽  
Edible Plant ◽  
Plant Fibers ◽  
High Genetic Diversity ◽  
Shotgun Metagenomics

AbstractPlant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.

scholarly journals Diversity and Function of the Eastern Oyster (Crassostrea virginica) Microbiome

2020 ◽  
Author(s):  
Zachary T. Pimentel ◽  
Keith Dufault-Thompson ◽  
Kayla T. Russo ◽  
Abigail K. Scro ◽  
Roxanna M. Smolowitz ◽  
...  
Keyword(s):  
Crassostrea Virginica ◽  
Functional Characterization ◽  
Eastern Oyster ◽  
High Variability ◽  
Metabolic Reconstruction ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Community Profiling ◽  
Genome Scale

ABSTRACTMarine invertebrate microbiomes play important roles in various host and ecological processes. However, a mechanistic understanding of host-microbe interactions is so far only available for a handful of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. A relatively low number of amplicon sequence variants (ASVs) were observed in oyster tissues compared to water samples, while high variability was observed across individual oysters and among different tissue types. Targeted metagenomic sequencing of the gut microbiota led to further characterization of a dominant bacterial taxon, the class Mollicutes, which was captured by the reconstruction of a metagenome-assembled genome (MAG). Genome-scale metabolic reconstruction of the oyster Mollicutes MAG revealed a reduced set of metabolic functions and a high reliance on the uptake of host-derived nutrients. A chitin degradation and an arginine deiminase pathway were unique to the MAG as compared to other closely related Mycoplasma genomes, indicating a distinct mechanism of carbon and energy acquisition by the oyster- associated Mollicutes. A systematic reanalysis of public eastern oyster-derived microbiome data revealed the Mollicutes as a ubiquitous taxon among adult oysters despite their general absence in larvae and biodeposit samples, suggesting potential horizontal transmission via an unknown mechanism.IMPORTANCEDespite well-documented biological significance of invertebrate microbiomes, a detailed taxonomic and functional characterization is frequently missing from many non-model marine invertebrates. By using 16S rRNA gene-based community profiling, shotgun metagenomics, and genome-scale metabolic reconstruction, this study provides an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica. Community profiling revealed a surprisingly low richness, as compared to surrounding seawater, and high variability among different tissue types and individuals. Reconstruction of a Mollicutes MAG enabled the phylogenomic positioning and functional characterization of the oyster-associated Mollicutes. Comparative analysis of the adult oyster gut, biodeposits, and oyster larvae samples indicated the potentially ubiquitous associations of the Mollicutes taxon with adult oysters. To the best of our knowledge, this study represented the first metagenomics derived functional inference of the eastern oyster microbiome. An integrated analytical procedure was developed for the functional characterization of microbiomes in other non-model host species.

scholarly journals Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiangning Bai ◽  
Aswathy Narayanan ◽  
Piotr Nowak ◽  
Shilpa Ray ◽  
Ujjwal Neogi ◽  
...  
Keyword(s):  
Antiretroviral Therapy ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Human Gut ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Hiv 1

Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.

Effect of the endophytic plant growth promoting Enterobacter ludwigii EB4B on tomato growth

2020 ◽  
Vol 13 (2) ◽  
pp. 54-65 ◽  
Author(s):  
M.E.A. Bendaha ◽  
H.A. Belaouni
Keyword(s):  
Root Length ◽  
Biocontrol Agent ◽  
Growth Promotion ◽  
Dry Weight ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Plant Growth Promoting ◽  
Enterobacter Ludwigii ◽  
Tomato Growth

SummaryThis study aims to develop a biocontrol agent against Fusarium oxysporum f.sp. radicis-lycopersici (FORL) in tomato. For this, a set of 23 bacterial endophytic isolates has been screened for their ability to inhibit in vitro the growth of FORL using the dual plate assay. Three isolates with the most sound antagonistic activity to FORL have been qualitatively screened for siderophore production, phosphates solubilization and indolic acetic acid (IAA) synthesis as growth promotion traits. Antagonistic values of the three candidates against FORL were respectively: 51.51 % (EB4B), 51.18 % (EB22K) and 41.40 % (EB2A). Based on 16S rRNA gene sequence analysis, the isolates EB4B and EB22K were closely related to Enterobacter ludwigii EN-119, while the strain EB2A has been assigned to Leclercia adecarboxylata NBRC 102595. The promotion of tomato growth has been assessed in vitro using the strains EB2A, EB4B and EB22K in presence of the phytopathogen FORL. The treatments with the selected isolates increased significantly the root length and dry weight. Best results were observed in isolate EB4B in terms of growth promotion in the absence of FORL, improving 326.60 % of the root length and 142.70 % of plant dry weight if compared with untreated controls. In the presence of FORL, the strain EB4B improved both root length (180.81 %) and plant dry weight (202.15 %). These results encourage further characterization of the observed beneficial effect of Enterobacter sp. EB4B for a possible use as biofertilizer and biocontrol agent against FORL.

scholarly journals Gluconacetobacter diazotrophicus Pal5 Enhances Plant Robustness Status under the Combination of Moderate Drought and Low Nitrogen Stress in Zea mays L.

2021 ◽  
Vol 9 (4) ◽  
pp. 870
Author(s):  
Muhammad Aammar Tufail ◽  
María Touceda-González ◽  
Ilaria Pertot ◽  
Ralf-Udo Ehlers
Keyword(s):  
Zea Mays ◽  
Plant Growth ◽  
Zea Mays L ◽  
Growth Promotion ◽  
Nitrogen Stress ◽  
Rrna Gene ◽  
N Fixation ◽  
Gluconacetobacter Diazotrophicus ◽  
Maize Plants ◽  
Low Nitrogen

Plant growth promoting endophytic bacteria, which can fix nitrogen, plays a vital role in plant growth promotion. Previous authors have evaluated the effect of Gluconacetobacter diazotrophicus Pal5 inoculation on plants subjected to different sources of abiotic stress on an individual basis. The present study aimed to appraise the effect of G. diazotrophicus inoculation on the amelioration of the individual and combined effects of drought and nitrogen stress in maize plants (Zea mays L.). A pot experiment was conducted whereby treatments consisted of maize plants cultivated under drought stress, in soil with a low nitrogen concentration and these two stress sources combined, with and without G. diazotrophicus seed inoculation. The inoculated plants showed increased plant biomass, chlorophyll content, plant nitrogen uptake, and water use efficiency. A general increase in copy numbers of G. diazotrophicus, based on 16S rRNA gene quantification, was detected under combined moderate stress, in addition to an increase in the abundance of genes involved in N fixation (nifH). Endophytic colonization of bacteria was negatively affected by severe stress treatments. Overall, G. diazotrophicus Pal5 can be considered as an effective tool to increase maize crop production under drought conditions with low application of nitrogen fertilizer.

scholarly journals A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility

2020 ◽  
Author(s):  
Blake W. Stamps ◽  
Wanda J. Lyon ◽  
Adam P. Irvin ◽  
Nancy Kelley-Loughnane ◽  
Michael S. Goodson
Keyword(s):  
Pilot Study ◽  
16S Rrna ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Initial Study ◽  
Mitigation Strategies ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Traveler’S Diarrhea ◽  
Traveler's Diarrhea

AbstractTraveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

scholarly journals Isolation and Characterization of Phosphate-Solubilizing Bacteria from Mushroom Residues and their Effect on Tomato Plant Growth Promotion

2017 ◽  
Vol 66 (1) ◽  
pp. 57-65 ◽  
Author(s):  
Jian Zhang ◽  
Peng Cheng Wang ◽  
Ling Fang ◽  
Qi-An Zhang ◽  
Cong Sheng Yan ◽  
...  
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Wood Flour ◽  
Dry Weight ◽  
Rrna Gene ◽  
Plant Growth Promoting Bacteria ◽  
Phosphate Solubilizing Bacteria ◽  
Sequence Comparisons ◽  
Isolation And Characterization ◽  
Phosphate Solubilizing

Phosphorus is a major essential macronutrient for plant growth, and most of the phosphorus in soil remains in insoluble form. Highly efficient phosphate-solubilizing bacteria can be used to increase phosphorus in the plant rhizosphere. In this study, 13 isolates were obtained from waste mushroom residues, which were composed of cotton seed hulls, corn cob, biogas residues, and wood flour. NBRIP solid medium was used for isolation according to the dissolved phosphorus halo. Eight isolates produced indole acetic acid (61.5%), and six isolates produced siderophores (46.2%). Three highest phosphate-dissolving bacterial isolates, namely, M01, M04, and M11, were evaluated for their beneficial effects on the early growth of tomato plants (Solanum lycopersicum L. Wanza 15). Strains M01, M04, and M11 significantly increased the shoot dry weight by 30.5%, 32.6%, and 26.2%, and root dry weight by 27.1%, 33.1%, and 25.6%, respectively. Based on 16S rRNA gene sequence comparisons and phylogenetic positions, strains M01 and M04 belonged to the genus Acinetobacter, and strain M11 belonged to the genus Ochrobactrum. The findings suggest that waste mushroom residues are a potential resource of plant growth-promoting bacteria exhibiting satisfactory phosphate-solubilizing for sustainable agriculture.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

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.

Enhanced tomato plant growth in soil under reduced P supply through microbial inoculants and microbiome shifts

2019 ◽  
Vol 95 (9) ◽  
Author(s):  
Namis Eltlbany ◽  
Mohamed Baklawa ◽  
Guo-Chun Ding ◽  
Dinah Nassal ◽  
Nino Weber ◽  
...  
Keyword(s):  
Plant Growth ◽  
Root Growth ◽  
Growth Promotion ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Pseudomonas Sp ◽  
Tomato Plants ◽  
Soil P ◽  
Bacterial Inoculants

ABSTRACT Soil microbial communities interact with roots, affecting plant growth and nutrient acquisition. In the present study, we aimed to decipher the effects of the inoculants Trichoderma harzianum T-22, Pseudomonas sp. DSMZ 13134, Bacillus amyloliquefaciens FZB42 or Pseudomonas sp. RU47 on the rhizosphere microbial community and their beneficial effects on tomato plants grown in moderately low phosphorous soil under greenhouse conditions. We analyzed the plant mass, inoculant colony forming units and rhizosphere communities on 15, 22, 29 and 43 days after sowing. Selective plating showed that the bacterial inoculants had a good rhizocompetence and accelerated shoot and root growth and nutrient accumulation. 16S rRNA gene fingerprints indicated changes in the rhizosphere bacterial community composition. Amplicon sequencing revealed that rhizosphere bacterial communities from plants treated with bacterial inoculants were more similar to each other and distinct from those of the control and the Trichoderma inoculated plants at harvest time, and numerous dynamic taxa were identified. In conclusion, likely both, inoculants and the rhizosphere microbiome shifts, stimulated early plant growth mainly by improved spatial acquisition of available nutrients via root growth promotion. At harvest, all tomato plants were P-deficient, suggesting a limited contribution of inoculants and the microbiome shifts to the solubilization of sparingly soluble soil P.

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