Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank’s and seed-originated microbiome recruitment depend on both plants’ genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.

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Rhizosphere Microbiome Regulates the Growth of Mustard under Organic Greenhouse Cultivation

Agriculture ◽

10.3390/agriculture11100987 ◽

2021 ◽

Vol 11 (10) ◽

pp. 987

Author(s):

Ting-Chung Liu ◽

Hui-Mei Peng ◽

Seth Wollney ◽

Chang-Hui Shen

Keyword(s):

Soil Microbiome ◽

Physiochemical Properties ◽

Tropical Regions ◽

Microbiome Composition ◽

Vegetable Growth ◽

Rhizosphere Microbiome ◽

Organic Cultivation ◽

Greenhouse Cultivation ◽

Next Generation Sequencing Ngs ◽

The Impact

Organic cultivation can improve soil fertility and biodiversity through the preservation of soil organic matter. Meanwhile, greenhouse cultivation can provide a controlled environment and therefore enables the management of every aspect of plant growth. In recent years, the combination of organic and greenhouse cultivation has slowly become a popular option in tropical regions to prevent the unpredictable impact of weather. Although it is known that organic cultivation significantly increases the density and species of microorganisms, the impact of soil microbiome on short-term vegetable growth under organic greenhouse cultivation is still not elucidated. In this study, we examined soil physiochemical properties as well as the rhizosphere microbiome from healthy and diseased mustard plants under organic greenhouse cultivation. Through next generation sequencing (NGS) analysis, our results revealed that the rhizosphere microbiome structure of healthy mustard plants was significantly different from those of the diseased mustard plants under organic greenhouse cultivation. Our findings suggest that soil microbiome composition can influence the growth of the vegetable significantly. As such, we have shown the impact of soil microbiome on vegetable growth under organic greenhouse cultivation and provide a possible strategy for sustainable agriculture.

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Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Applied and Environmental Microbiology ◽

10.1128/aem.00956-12 ◽

2012 ◽

Vol 78 (17) ◽

pp. 6153-6160 ◽

Cited By ~ 56

Author(s):

Elizabeth A. Maga ◽

Prerak T. Desai ◽

Bart C. Weimer ◽

Nguyet Dao ◽

Dietmar Kültz ◽

...

Keyword(s):

Human Milk ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Gut Health ◽

Content Type ◽

Microbiome Composition ◽

The Impact ◽

Over Time

ABSTRACTHuman milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels ofFirmicutes(Clostridia) declined whereas those ofBacteroidetesincreased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P< 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (BifidobacteriaceaeandLactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae,Streptococcaceae,Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

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Bioactive Diterpenoids Impact the Composition of the Root-Associated Microbiome in Maize (Zea mays)

10.21203/rs.3.rs-21333/v1 ◽

2020 ◽

Author(s):

Katherine M. Murphy ◽

Joseph Ewards ◽

Katherine B. Louie ◽

Benjamin P. Bowen ◽

Venkatesan Sundaresan ◽

...

Keyword(s):

Zea Mays ◽

Molecular Mechanisms ◽

Bacterial Community Composition ◽

16S Rrna Gene Sequencing ◽

Chemical Defenses ◽

Rrna Gene ◽

Wild Type ◽

Microbiome Composition ◽

Rhizosphere Microbiome ◽

Maize Varieties

Abstract Background : Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges. This includes interactions with soil-dwelling microbial communities, where plants may exchange sugars for important nutrients and protection against environmental perturbations, directly benefitting plant fitness. However, the molecular mechanisms underlying these plant-microbe interactions often remain elusive. Results : In this study, we report that maize ( Zea mays ) specialized diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 ( anther ear 2 ), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. Under well-watered conditions, the Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. By contrast, there was no difference in the microbiome composition between the mutant and wild-type was observed under drought stress. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other metabolome alterations. Conclusions : Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

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The Effect of Antiretroviral Therapy Initiation on the Vaginal Microbiome in HIV-Infected Women

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz328 ◽

2019 ◽

Vol 6 (9) ◽

Cited By ~ 2

Author(s):

Cindy M Liu ◽

Zoe R Packman ◽

Alison G Abraham ◽

David M Serwadda ◽

Fred Nalugoda ◽

...

Keyword(s):

Antiretroviral Therapy ◽

Immune Reconstitution ◽

Bacterial Load ◽

Sub Saharan Africa ◽

Rrna Gene ◽

Host Immune System ◽

Vaginal Microbiome ◽

Microbiome Composition ◽

Art Initiation ◽

The Impact

Abstract Background The impact of antiretroviral therapy (ART) initiation on the vaginal microbiome is unknown. This is of particular importance among women living in sub-Saharan Africa. Understanding this relationship could help elucidate if and how the host immune system interacts with the vaginal microbiome. Methods The vaginal microbiome of HIV-1/HSV-2-coinfected women (n = 92) in Uganda was evaluated from self-collected vaginal swabs 1 month pre-ART and at 4 and 6 months post–ART initiation. The vaginal microbiome was characterized by 16S rRNA gene-based sequencing and quantitative polymerase chain reaction. Vaginal community state types (CSTs) were identified using proportional abundance data. Changes in microbiome composition were assessed with permutational analyses of variance (PerMANOVA). Results Five vaginal CSTs were identified, which varied significantly by bacterial load (P < .01): CST-1 was characterized by Lactobacillus iners, CST-2 by Gardnerella, CST-3 by Gardnerella and Prevotella, CST-4 by Lactobacillus crispatus, and CST-5 was highly diverse. Vaginal microbiome composition also did not change significantly after ART initiation (P = .985). Immune reconstitution after ART initiation did not affect vaginal microbiome CST assignment (P = .722) or individual-level changes in bacterial load (log response ratio [interquartile range], –0.50 [–2.75 to 0.38] vs –0.29 [–2.03 to 1.42]; P = .40). Conclusions The vaginal microbiome of HIV-infected women was not affected by the initiation of ART or immune reconstitution in this observational study. Further research is needed to explore the long-term effects of ART treatment on the vaginal microbiome.

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The Impact of Traumatic Brain Injury on Microbiome Composition: A Systematic Review

Biological Research For Nursing ◽

10.1177/1099800420943961 ◽

2020 ◽

Vol 22 (4) ◽

pp. 495-505

Author(s):

Nihar Pathare ◽

Sandhra Sushilkumar ◽

Lauren Haley ◽

Shivani Jain ◽

Nicole (Nico) Osier

Keyword(s):

Systematic Review ◽

Gut Microbiome ◽

Animal Studies ◽

Brain Injuries ◽

Small Sample ◽

Therapeutic Interventions ◽

Rrna Gene ◽

Bacterial Populations ◽

Microbiome Composition ◽

The Impact

Traumatic brain injuries (TBIs) are a significant health problem, impacting millions of people every year. Although emerging evidence suggests that the composition of the gut microbiome is altered after TBI, no systematic review has been published on this topic. The objective of the present systematic review is to analyze publications that evaluate the impact of TBI on gut microbiome composition. Research articles were pulled from seven databases. The systematic review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. In order for publications to be eligible for this review, they had to (1) report on original human- or animal-subjects research, (2) evaluate the impact of TBI on the microbiome, and (3) be written in English and (4) be published in a peer-reviewed journal. Of the seven articles that met these criteria, one involved human participants, while the other six reported on experimental animal studies. All studies found changes in the gut microbiome following TBI, with similar changes in bacterial populations observed across studies. The limitations of these studies included the use of primarily male animals, limitations of 16 S rRNA gene sequencing, and small sample sizes. This review was also limited by the small pool of studies conducted in this area. In summary, changes in bacterial populations of the gut microbiome, specifically increases in proteobacteria and firmicutes, were observed across the studies. By evaluating the changes in the microbiome resulting from TBI, potential therapeutic interventions could be explored.

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SARS-CoV-2 Infection and Inflammatory Response in a Twin Pregnancy

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18063075 ◽

2021 ◽

Vol 18 (6) ◽

pp. 3075

Author(s):

Andrea Trombetta ◽

Manola Comar ◽

Alberto Tommasini ◽

Melania Canton ◽

Giuseppina Campisciano ◽

...

Keyword(s):

Inflammatory Response ◽

Pregnant Women ◽

Vertical Transmission ◽

Twin Pregnancy ◽

Immunological Response ◽

Host Susceptibility ◽

Fetal Mortality ◽

Vaginal Microbiome ◽

Microbiome Composition ◽

The Impact

There is growing literature about the SARS-CoV-2 pathogenetic effects exerted during pregnancy and whether vertical transmission or premature birth is possible. It is not well known whether changes in the immune system of pregnant women may lead to a marked susceptibility to infectious processes and the risk of adverse maternal and neonatal complications such as preterm birth, spontaneous abortion, hospitalization in an intensive care unit, transmission to the fetus or newborns, and fetal mortality are poorly understood. Along with this ongoing debate, it is not well defined whether, during pregnancy, the role of host susceptibility in producing a specific inflammatory response to SARS-CoV-2 may represent distinctive markers of risk of vertical transmission. Furthermore, SARS-CoV-2 impact on the vaginal microbiome has not yet been described, despite mounting evidence on its possible effect on the gastrointestinal microbiome and its influence on infectious diseases and preterm labor. This report describes the impact of SARS-CoV-2 on a twin pregnancy diagnosed with infection at the third trimester of gestation including tissue infections, inflammatory response, antibody production, cytokine concentration, and vaginal microbiome composition. We identified a pattern of cytokines including IL1-Ra, IL-9 G-CSF, IL-12, and IL-8 differently expressed, already associated with previously infected patients. We detected a similar concentration of almost all the cytokines tested in both twins, suggesting that the SARS-CoV-2-induced cytokine storm is not substantially impaired during the placental passage. The analysis of the vaginal microbiome did not show relevant signs of dysbiosis, similar to other healthy pregnant women and twin healthy pregnancies. The aim of this report was to analyze the immunological response against SARS-CoV-2 infection and virus tissue tropism in a twin pregnancy.

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Impact of Novel Coronavirus (COVID-19) on Pregnant Women: A Review

Coronaviruses ◽

10.2174/2666796701999201116123457 ◽

2020 ◽

Vol 01 ◽

Author(s):

Saima Habeeb ◽

Manju Chugani

Keyword(s):

Pregnant Women ◽

Vertical Transmission ◽

Respiratory Infections ◽

Age Groups ◽

Well Being ◽

Fetal Outcome ◽

Global Public Health ◽

Coronavirus Infection ◽

Novel Coronavirus ◽

The Impact

: The novel coronavirus infection (COVID‐19) is a global public health emergency.Since its outbreak in Wuhan, China in December 2019, the infection has spread at an alarming rate across the globe and humans have been locked down to their countries, cities and homes. As of now, the virus has affected over 20million people globally and has inflicted over 7 lac deaths. Nevertheless, the recovery rate is improving with each passing day and over 14 million people have recuperated so far. The statistics indicate that nobody is immune to the disease as the virus continues to spread among all age groups; newborns to the elders, and all compartmentsincluding pregnant women. However, pregnant women may be more susceptible to this infection as they are, in general, highly vulnerable to respiratory infections. There is no evidence for vertical transmission of the COVID-19 virus among pregnant women, but an increased prevalence of preterm deliveries. Besides this, the COVID-19 may alter immune response at the maternal-fetal interface and affect the well-being of mothers as well as infants. Unfortunately, there is limited evidence available in the open literature regarding coronavirus infection during pregnancy and it now appears that certain pregnant women have infected during the present 2019-nCoV pandemic. In this short communication, we study the impact of the COVID-19 infection on vertical transmission and fetal outcome among pregnant women.

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Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11353-4 ◽

2021 ◽

Author(s):

Annemarie Siebert ◽

Katharina Hofmann ◽

Lena Staib ◽

Etienne V. Doll ◽

Siegfried Scherer ◽

...

Keyword(s):

Sample Preparation ◽

Dna Extraction ◽

Raw Milk ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Dna ◽

Microbiome Analysis ◽

Eukaryotic Dna ◽

Selective Lysis ◽

The Impact

Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

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A Cross-Metabolomic Approach Shows that Wheat Interferes with Fluorescent Pseudomonas Physiology through Its Root Metabolites

Metabolites ◽

10.3390/metabo11020084 ◽

2021 ◽

Vol 11 (2) ◽

pp. 84

Author(s):

Laura Rieusset ◽

Marjolaine Rey ◽

Florence Gerin ◽

Florence Wisniewski-Dyé ◽

Claire Prigent-Combaret ◽

...

Keyword(s):

Secondary Metabolites ◽

Host Plant ◽

Soil Microorganisms ◽

Wheat Root ◽

Bioactive Metabolites ◽

Root Extracts ◽

Fluorescent Pseudomonas ◽

Health And Development ◽

The Impact ◽

Metabolomic Approach

Roots contain a wide variety of secondary metabolites. Some of them are exudated in the rhizosphere, where they are able to attract and/or control a large diversity of microbial species. In return, the rhizomicrobiota can promote plant health and development. Some rhizobacteria belonging to the Pseudomonas genus are known to produce a wide diversity of secondary metabolites that can exert a biological activity on the host plant and on other soil microorganisms. Nevertheless, the impact of the host plant on the production of bioactive metabolites by Pseudomonas is still poorly understood. To characterize the impact of plants on the secondary metabolism of Pseudomonas, a cross-metabolomic approach has been developed. Five different fluorescent Pseudomonas strains were thus cultivated in the presence of a low concentration of wheat root extracts recovered from three wheat genotypes. Analysis of our metabolomic workflow revealed that the production of several Pseudomonas secondary metabolites was significantly modulated when bacteria were cultivated with root extracts, including metabolites involved in plant-beneficial properties.

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COVID-19: Uncertainties from Conception to Birth

Revista Brasileira de Ginecologia e Obstetrícia / RBGO Gynecology and Obstetrics ◽

10.1055/s-0040-1721856 ◽

2021 ◽

Vol 43 (01) ◽

pp. 054-060

Author(s):

Bruno Ramalho de Carvalho ◽

Karina de Sá Adami ◽

Walusa Assad Gonçalves-Ferri ◽

Marise Samama ◽

Rui Alberto Ferriani ◽

...

Keyword(s):

Pregnant Women ◽

Present Article ◽

Vertical Transmission ◽

Scientific Information ◽

Obstetric Outcomes ◽

Reproductive Events ◽

The Impact ◽

Initial Impressions ◽

Quality Evidence

AbstractScientific information on the impact of the new coronavirus (SARS-CoV-2) on the health of pregnant women, fetuses and newborns is considered of limited confidence, lacking good-quality evidence, and drawing biased conclusions. As a matter of fact, the initial impressions that the evolution of COVID-19 was no different between pregnant and non-pregnant women, and that SARS-CoV-2 was not vertically transmitted, are confronted by the documentation of worsening of the disease during pregnancy, poor obstetric outcomes, and the possibility of vertical transmission. The present article aims to compile the data available on the association of COVID-19 and reproductive events, from conception to birth.

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