scholarly journals Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

2019 ◽  
Vol 117 (2) ◽  
pp. 1148-1159 ◽  
Author(s):  
Norma M. Morella ◽  
Francis Cheng-Hsuan Weng ◽  
Pierre M. Joubert ◽  
C. Jessica E. Metcalf ◽  
Steven Lindow ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Amplicon Sequencing ◽  
Host Genotype ◽  
Microbial Composition ◽  
Internal Transcribed Spacer Region ◽  
Tomato Plants ◽  
16S Amplicon Sequencing ◽  
Host Evolution ◽  
Plant Microbiome

There is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across 5 plant genotypes for 4 45-d passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (internal transcribed spacer region amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment, suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted within the experimental setting. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond. In light of the consistent response of the microbiome to selection in the absence of reciprocal host evolution (coevolution) described here, future studies should address how such adaptation influences host health.

scholarly journals Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

2019 ◽  
Author(s):  
Norma M. Morella ◽  
Francis Cheng-Hsuan Weng ◽  
Pierre M. Joubert ◽  
C. Jessica E. Metcalf ◽  
Steven Lindow ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Amplicon Sequencing ◽  
Host Genotype ◽  
Microbial Composition ◽  
Plant Host ◽  
Independent Manner ◽  
16S Amplicon Sequencing ◽  
The Impact ◽  
Plant Microbiome

AbstractThere is increasing interest in the plant microbiome as it relates to both plant health and agricultural sustainability. One key unanswered question is whether we can select for a plant microbiome that is robust after colonization of target hosts. We used a successive passaging experiment to address this question by selecting upon the tomato phyllosphere microbiome. Beginning with a diverse microbial community generated from field-grown tomato plants, we inoculated replicate plants across five plant genotypes for four eight-week long passages, sequencing the microbial community at each passage. We observed consistent shifts in both the bacterial (16S amplicon sequencing) and fungal (ITS amplicon sequencing) communities across replicate lines over time, as well as a general loss of diversity over the course of the experiment suggesting that much of the naturally observed microbial community in the phyllosphere is likely transient or poorly adapted. We found that both host genotype and environment shape microbial composition, but the relative importance of genotype declines through time. Furthermore, using a community coalescence experiment, we found that the bacterial community from the end of the experiment was robust to invasion by the starting bacterial community. These results highlight that selecting for a stable microbiome that is well adapted to a particular host environment is indeed possible, emphasizing the great potential of this approach in agriculture and beyond.Significance StatementThere is great interest in selecting for host-associated microbiomes that confer particular functions to their host, and yet it remains unknown whether selection for a robust and stable microbiome is possible. Here, we use a microbiome passaging approach to measure the impact of host-mediated selection on the tomato phyllosphere (above ground) microbiome. We find robust community selection across replicate lines that is shaped by plant host genotype in early passages, but changes in a genotype-independent manner in later passages. Work such as ours is crucial to understanding the general principles governing microbiome assembly and adaptation, and is widely applicable to both sustainable agriculture and microbiome-related medicine.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

scholarly journals Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

2020 ◽  
Author(s):  
Saeed Keshani Langroodi ◽  
Yemin Lan ◽  
Ben Stenuit ◽  
Gail Rosen ◽  
Joseph B Hughes ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Metagenomic Data ◽  
Military Conflict ◽  
Nitro Explosives ◽  
And Function ◽  
Aerobic And Anaerobic

Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented.

Sa244 INFLUENCE OF HELICOBACTER PYLORI ON THE MICROBIAL COMPOSITION OF HUMAN GASTRIC MUCOSA: ANALYSIS BASED ON DNA AND RNA 16S AMPLICON SEQUENCING

2021 ◽  
Vol 160 (6) ◽  
pp. S-463
Author(s):  
Elena Kupriyanova ◽  
Maria Markelova ◽  
Sayar Abdulkhakov ◽  
Tatyana Grigoryeva ◽  
Airat Safin ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Gastric Mucosa ◽  
Amplicon Sequencing ◽  
Human Gastric Mucosa ◽  
Microbial Composition ◽  
Dna And Rna ◽  
16S Amplicon Sequencing

scholarly journals Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

2015 ◽  
Vol 81 (7) ◽  
pp. 2525-2533 ◽  
Author(s):  
Daniel J. O'Sullivan ◽  
Paul D. Cotter ◽  
Orla O'Sullivan ◽  
Linda Giblin ◽  
Paul L. H. McSweeney ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Production Cycle ◽  
Microbial Composition ◽  
Temporal And Spatial Distribution ◽  
Content Type ◽  
Temporal And Spatial

ABSTRACTWe sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the generaThermus,Pseudoalteromonas, andBifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.

scholarly journals Dietary cardoon meal modulates rumen biohydrogenation and bacterial community in lambs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Saheed A. Salami ◽  
Bernardo Valenti ◽  
Giuseppe Luciano ◽  
Massimiliano Lanza ◽  
Ngozi M. Umezurike-Amahah ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Microbial Community ◽  
Bacterial Community ◽  
Amplicon Sequencing ◽  
Oil Extraction ◽  
Rumen Fermentation ◽  
Cynara Cardunculus ◽  
Genus Level ◽  
Fa Composition ◽  
Branched Chain

AbstractCardoon meal is a by-product of oil extraction from the seeds of Cynara cardunculus and can serve as a novel alternative feedstuff for ruminants. This study examined the rumen fermentation, biohydrogenation of fatty acids (FA) and microbial community in lambs fed a concentrate diet containing 15% dehydrated lucerne (CON, n = 8) or cardoon meal (CMD, n = 7) for 75 days pre-slaughter. Diets did not influence rumen fermentation characteristics and the abundance of bacteria, methanogens, fungi, or protozoa. Rumen digesta in CMD-fed lambs displayed a higher concentration of total saturated FA and lower total odd- and branched-chain FA and monounsaturated FA. Feeding CMD decreased total trans-18:1 isomer and the ratio of trans-10 to trans-11 C18:1, known as the “trans-10 shift”. Amplicon sequencing indicated that the rumen bacterial community in CMD-fed lambs had lower diversity and a higher relative phyla abundance of Proteobacteria at the expense of Bacteroidetes and Fibrobacteres. At the genus level, CMD mediated specific shifts from Prevotella, Alloprevotella, Solobacterium and Fibrobacter to Ruminobacter, suggesting that these genera may play important roles in biohydrogenation. Overall, these results demonstrate that cardoon meal can be used as a feedstuff for ruminants without negatively affecting rumen fermentation and microbiota but its impact on biohydrogenation may influence the FA composition in meat or milk.

scholarly journals Microbial composition of enigmatic bird parasites:WolbachiaandSpiroplasmaare the most important bacterial associates of quill mites (Acari: Syringophilidae)

2018 ◽  
Author(s):  
Eliza Glowska ◽  
Zuzanna K. Filutowska ◽  
Miroslawa Dabert ◽  
Michael Gerth
Keyword(s):  
Subcutaneous Tissue ◽  
Detection Threshold ◽  
Bird Species ◽  
Amplicon Sequencing ◽  
Biological Properties ◽  
Mite Species ◽  
Symbiotic Association ◽  
Microbial Composition ◽  
Quill Mites ◽  
16S Amplicon Sequencing

AbstractThe microbiome is an integral component of many animal species, potentially affecting behaviour, physiology, and other biological properties. Despite this importance, bacterial communities remain vastly understudied in many groups of invertebrates, including mites. Quill mites (Acariformes: Syringophilidae) are a poorly known group of permanent bird ectoparasites that occupy quills of feathers and feed on bird subcutaneous tissue and fluids. Most species have strongly female biased sex ratios and it was hypothesized that this is caused by endosymbiotic bacteria. Their peculiar lifestyle further makes them potential vectors for bird diseases. Previously,Anaplasma phagocytophilumand a high diversity ofWolbachiastrains were detected in quill mites via targeted PCR screens. Here, we use an unbiased 16S amplicon sequencing approach to determine other Bacteria that potentially impact quill mite biology.We performed 16S V4 amplicon sequencing of 126 quill mite individuals from eleven species parasitizing twelve bird species (four families) of passeriform birds. In addition toWolbachia, we foundSpiroplasmaas potential symbiont of quill mites. Interestingly, consistently highSpiroplasmatitres were only found in individuals of two mite species associated with finches of the genusCardfuelis, suggesting a history of horizontal transfers ofSpiroplasmavia the bird host. Furthermore, there was evidence forSpiroplasmanegatively affectingWolbachiatitres. We found no evidence for the previously reportedAnaplasmain quill mites, but detected the potential pathogensBrucellaandBartonellaat low abundances. Other amplicon sequence variants (ASVs) could be assigned to a diverse number of bacterial taxa, including several that were previously isolated from bird skin. We observed a relatively uniform distribution of these ASVs across mite taxa and bird hosts, i.e, there was a lack of host-specificity for most detected ASVs. Further, many frequently found ASVs were assigned to taxa that show a very broad distribution with no strong prior evidence for symbiotic association with animals. We interpret these findings as evidence for a scarcity or lack of resident microbial associates (other than inherited symbionts) in quill mites, or for abundances of these taxa below our detection threshold.

scholarly journals Exploring Yak (Bos grunniens) Rumen Bacterial and Fungal Communities from 5 Days after Birth to Adulthood

2022 ◽  
Author(s):  
Shuli Yang ◽  
Guangrong Zhang ◽  
Mingyue Deng ◽  
Liyuan Sun ◽  
Shichun He ◽  
...  
Keyword(s):  
Microbial Community ◽  
Anaerobic Bacteria ◽  
Age Groups ◽  
Amplicon Sequencing ◽  
Meat Production ◽  
Gradual Change ◽  
Microbial Composition ◽  
Plant Fibers ◽  
Rumen Microorganisms ◽  
Facultative Anaerobic Bacteria

Abstract The gut microbial community of mammals, especially ruminants, plays an important role at different ages of the host. Ruminants have a unique compartment in their digestive tract; the rumen, comprising microorganisms that can effectively decompose plant fibers for the host to transform into milk and for growth and development, which is important for meat production. Colonization of rumen microorganisms is closely related to host developmental stage and affects host performance production. There is little information regarding initial colonization and subsequent changes of the rumen microbial population in wild grazing animals, from birth to adulthood. This study investigated the rumen bacterial and fungal populations of grazing yaks in five experimental groups, ranging from a few days after birth to adulthood using amplicon sequencing. Results indicated that rumen microbial communities of these yaks undergo a gradual change from 5 to 180 days after birth, with the bacterial and fungal diversity stabilizing at the age of 2 years. Additionally, Ruminococcus was detected in 5-day-old yak rumens, with a high percentage of Penicillium and other microbial species are important for normal rumen function detected in the adult rumen. The changes to the yak rumen microbial community after birth were reflected in the increased anaerobic fiber degradation group, and decreased aerobic and facultative anaerobic bacteria. Microbial diversity and abundance in the yak rumen increased with age. Rumen microbial composition of 6-month and 2-year-old yaks had obvious homogeneity. There were some differences in dominant rumen microorganisms among the different age groups. Further studies are required to confirm the functions of these differential and dominant microorganisms in each age group.

scholarly journals Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea

2019 ◽  
Vol 85 (13) ◽  
Author(s):  
Bliss Ursula Furtado ◽  
Marcin Gołębiewski ◽  
Monika Skorupa ◽  
Piotr Hulisz ◽  
Katarzyna Hrynkiewicz
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Microbial Community Composition ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Salicornia Europaea ◽  
Core Microbiome ◽  
Plant Organs ◽  
Content Type ◽  
Microbial Groups

ABSTRACT We examined Salicornia europaea, a nonmycorrhizal halophyte associated with specific and unique endophytic bacteria and fungi. The microbial community structure was analyzed at two sites differing in salinization history (anthropogenic and naturally saline site), in contrasting seasons (spring and fall) and in two plant organs (shoots and roots) via 16S rRNA and internal transcribed spacer amplicon sequencing. We observed distinct communities at the two sites, and in shoots and roots, while the season was of no importance. The bacterial community was less diverse in shoot libraries than in roots, regardless of the site and season, whereas no significant differences were observed for the fungal community. Proteobacteria and Bacteroidetes dominated bacterial assemblages, and Ascomycetes were the most frequent fungi. A root core microbiome operational taxonomic unit belonging to the genus Marinimicrobium was identified. We detected a significant influence of the Salicornia bacterial community on the fungal one by means of cocorrespondence analysis. In addition, pathways and potential functions of the bacterial community in Salicornia europaea were inferred and discussed. We can conclude that bacterial and fungal microbiomes of S. europaea are determined by the origin of salinity at the sites. Bacterial communities seemed to influence fungal ones, but not the other way around, which takes us closer to understanding of interactions between the two microbial groups. In addition, the plant organs of the halophyte filter the microbial community composition. IMPORTANCE Endophytes are particularly fascinating because of their multifaceted lifestyle, i.e., they may exist as either free-living soil microbes or saprobic ones or pathogens. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host’s adaptation to adverse environmental conditions, which may be of importance in agriculture.

scholarly journals Effects of Microcystin-LR on Metabolic Functions and Structure Succession of Sediment Bacterial Community under Anaerobic Conditions

Toxins ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 183 ◽  
Author(s):  
Qin Ding ◽  
Kaiyan Liu ◽  
Zhiquan Song ◽  
Rongli Sun ◽  
Juan Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Metabolic Activity ◽  
Amplicon Sequencing ◽  
Anaerobic Conditions ◽  
Treatment Frequency ◽  
Metabolic Functions ◽  
Cyanobacteria Blooms ◽  
16S Amplicon Sequencing ◽  
The Relationship ◽  
Sediment Bacterial Community

Microcystins (MCs), which are produced by harmful cyanobacteria blooms, pose a serious threat to environmental health. However, the effect of MCs on the bacterial community under anaerobic conditions is still unclear. This study examined the dynamic changes of MC-degrading capacity, metabolic activity, and structure of the bacterial community in lake sediment repeatedly treated with 1 mg/L microcystin-LR (MC-LR) under anaerobic conditions. The results showed that the MC-degrading capacity of the bacterial community was increased nearly three-fold with increased treatment frequency. However, the metabolic profile behaved in exactly opposite trend, in which the overall carbon metabolic activity was inhibited by repeated toxin addition. Microbial diversity was suppressed by the first addition of MC-LR and then gradually recovered. The 16S amplicon sequencing showed that the dominant genera were changed from Exiguobacterium and Acinetobacter to Prosthecobacter, Dechloromonas, and Agrobacterium. Furthermore, the increase in the relative abundance of Dechloromonas, Pseudomonas, Hydrogenophaga, and Agrobacterium was positively correlated with the MC-LR treatment times. This indicates that they might be responsible for MC degradation under anaerobic conditions. Our findings reveal the relationship between MC-LR and the sediment bacterial community under anaerobic conditions and indicate that anaerobic biodegradation is an effective and promising method to remediate MCs pollution.

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