Exposure to Parasitic Protists and Helminths Changes the Intestinal Community Structure of Bacterial Communities in a Cohort of Mother-Child Binomials from a Semirural Setting in Mexico

The impact of intestinal eukaryotes on the prokaryotic microbiome composition of asymptomatic carriers has not been extensively explored, especially in infants and mothers with multiple parasitic infections. In this work, we studied the relationship between protist and helminth parasite colonization and the intestinal microbiota structure in an asymptomatic population of mother-child binomials from a semirural community in Mexico.

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Bacterial communities of the rhizosphere and endorhiza associated with field-grown cucumber plants inoculated with a plant growth-promoting rhizobacterium or its genetically modified derivative

Canadian Journal of Microbiology ◽

10.1139/m97-048 ◽

1997 ◽

Vol 43 (4) ◽

pp. 344-353 ◽

Cited By ~ 48

Author(s):

W. F. Mahaffee ◽

J. W. Kloepper

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Genetically Modified ◽

Acid Methyl Ester ◽

Wild Type ◽

Natural Ecosystems ◽

Genus Level ◽

Plant Growth Promoting ◽

The Impact

The future use of genetically modified microorganisms in the environment will be dependent on the ability to assess potential or theoretical risks associated with their introduction into natural ecosystems. To assess potential risks, several ecological parameters must be examined, including the impact of the introduced genetically modified organism on the microbial communities associated with the environment into which the introduction will occur. A 2-year field study was established to examine whether the indigenous bacterial communities of the rhizosphere and endorhiza (internal root tissues) were affected differently by the introduction of an unaltered wild type and its genetically modified derivative. Treatments consisted of the wild-type strain Pseudomonas fluorescens 89B-27 and a bioluminescent derivative GEM-8 (89B-27::Tn4431). Cucumber root or seed samples were taken 0, 7, 14, 21, 35, and 70 days after planting (DAP) in 1994 and 0, 7, 14, 28, 42, and 70 DAP in 1995. Samples were processed to examine the bacterial communities of both the rhizosphere and endorhiza. Over 7200 bacterial colonies were isolated from the rhizosphere and endorhiza and identified using the Sherlock System (Microbial ID, Inc.) for fatty acid methyl ester analysis. Community structure at the genus level was assessed using genera richness and Hill's diversity numbers, N1 and N2. The aerobic–heterotrophic bacterial community structure at the genus level did not significantly vary between treatments but did differ temporally. The data indicate that the introduction of the genetically modified derivative of 89B-27 did not pose a greater environmental risk than its unaltered wild type with respect to aerobic–heterotrophic bacterial community structure.Key words: diversity, ecology, PGPR, Pseudomonas, root colonizaton, GEM.

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Diversity of Epiphytic Bacterial Communities Associated with Adriatic Fucacean Species Phycosphere

Journal of Marine Science and Engineering ◽

10.3390/jmse8120967 ◽

2020 ◽

Vol 8 (12) ◽

pp. 967

Author(s):

Maria Blažina ◽

Ljiljana Iveša ◽

Ksenija Matošović ◽

Emina Pustijanac ◽

Massimo Devescovi ◽

...

Keyword(s):

Fatty Acids ◽

Community Structure ◽

Polyunsaturated Fatty Acids ◽

Bacterial Communities ◽

Saturated Fatty Acids ◽

Strong Relationship ◽

Scaling Analysis ◽

Biological Interactions ◽

Cystoseira Compressa ◽

The Relationship

The aim of the study was to explore the relationship between membrane-regulating functional lipids of three fucacean species and their associated epiphytic bacterial communities. The analyzed algae Treptacantha barbata, Carpodesmia crinita and Cystoseira compressa, formerly classified under the Cystoseira genus, are indigenous to the Adriatic Sea. The thalli of sampled Fucales species were divided into perennial and annual parts. T. barbata and C. crinita show high contents of mono- and polyunsaturated fatty acids but, however, show a clear distinction between branches, cauloids and apical parts. Along with the highest unsaturation degree (4.32), the C. crinita branches and apical parts demonstrated high proportion of both C18 and C20 polyunsaturated fatty acids, with eicosapentaenoic (C20:5 n-3) and arachidonic (C20:4 n-6) fatty acids up to 5.46% and 13.82%, respectively. The highest proportion of saturated fatty acids was found in thalli of C. compressa, particularly on cauloids and old branches (≥90%). The similarity profile routine analysis of fatty acids and microbial community structure has shown clear separation of the cauloids and apical parts from the branches of C. crinita and T. barbata. Based on the nonmetric multidimensional scaling analysis several representatives of the Gammaproteobacteria class, identified as Vibrionales (Vibrio), Cellvibrionales and Xanthomonadales, which contributed strongly to the separation of T. barbata apical parts and branches, C. compressa receptacles and C. crinita branches from the T. barbata cauloids and C. crinita apical parts and cauloids. The highest richness in polyunsaturated fatty acids, in particular C18:3(n-3), C20:4(n-6) and C20:5(n-3), was observed on branches, accompanied by a distinctive epiphytic microbial structure dominated by numerous representatives with potentially beneficial biological activity. The results showed a strong relationship between fatty acid profiles of the analyzed species and phycosphere community structure, underlining the host physiological condition in shaping the biological interactions and maintaining a healthy microbiome, as well as compiling the ecophysiological and molecular research in order to better assess the resilience of the ecosystem.

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Healthy gut microbiota and long term health

Beneficial Microbes ◽

10.3920/bm2014.0072 ◽

2015 ◽

Vol 6 (2) ◽

pp. 173-179 ◽

Cited By ~ 6

Author(s):

Y. Vandenplas

Keyword(s):

Immune System ◽

Intestinal Microbiota ◽

Research Topic ◽

Intestinal Microbiome ◽

Microbiome Composition ◽

Immune Mediated ◽

The Impact ◽

Tremendous Impact ◽

Postnatal Factors

This review summarises how the composition of the gastro-intestinal microbiota depends on pre- and postnatal factors, and birth itself. The impact of method of delivery, feeding during infancy and medications, such as antibiotics and anti-acid medication, on the composition of the gastro-intestinal microbiota has clearly been shown. However, the duration of the impact of these factors is not well established. The gastro-intestinal microbiome composition is associated with many auto-immune mediated diseases. Although causality has not been obviously demonstrated, there is a strong tendency in this direction. Nevertheless, results of the manipulation of the gastro-intestinal microbiome composition in these conditions are often disappointing. A better understanding on factors determining the longterm composition of the gastro-intestinal microbiome and its health consequences are a priority research topic. A better understanding of the association between the microbiome and the immune system may have a tremendous impact on general health.

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Haemoproteusinfected birds have increased lifetime reproductive success

Parasitology ◽

10.1017/s0031182015000256 ◽

2015 ◽

Vol 142 (8) ◽

pp. 1033-1043 ◽

Cited By ~ 15

Author(s):

M. ZYLBERBERG ◽

E. P. DERRYBERRY ◽

C. W. BREUNER ◽

E. A. MACDOUGALL-SHACKLETON ◽

J. M. CORNELIUS ◽

...

Keyword(s):

Reproductive Success ◽

Lifetime Reproductive Success ◽

Parasitic Infections ◽

Host Fitness ◽

Return Rates ◽

Long Term Study ◽

In The Wild ◽

The Impact ◽

The Relationship

SUMMARYThe impact of haematozoan infection on host fitness has received substantial attention since Hamilton and Zuk posited that parasites are important drivers of sexual selection. However, short-term studies testing the assumption that these parasites consistently reduce host fitness in the wild have produced contradictory results. To address this complex issue, we conducted a long-term study examining the relationship between naturally occurring infection withHaemoproteusandPlasmodium, and lifetime reproductive success and survival of Mountain White-crowned Sparrows. Specifically, we tested the hypothesis that birds infected with haematozoan parasites have reduced survival (as determined by overwinter return rates) and reproductive success. Contrary to expectation, there was no relationship betweenHaemoproteusandPlasmodiuminfection and reproduction or survival in males, nor was there a relationship betweenPlasmodiuminfection and reproduction in females. Interestingly,Haemoproteus-infected females had significantly higher overwinter return rates and these females fledged more than twice as many chicks during their lifetimes as did uninfected females. We discuss the impact of parasitic infections on host fitness in light of these findings and suggest that, in the case of less virulent pathogens, investment in excessive immune defence may decrease lifetime reproduction.

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Gut segments outweigh the diet in shaping the intestinal microbiome composition in grass carp Ctenopharyngodon idellus

10.1101/356030 ◽

2018 ◽

Author(s):

Wenwen Feng ◽

Jing Zhang ◽

Ivan Jakovlić ◽

Fan Xiong ◽

Shangong Wu ◽

...

Keyword(s):

Gut Microbiota ◽

Intestinal Microbiota ◽

Grass Carp ◽

Herbivorous Fish ◽

Limited Ability ◽

Microbiome Composition ◽

Sudan Grass ◽

Anoxic Environment ◽

The Impact ◽

Intestinal Compartments

ABSTRACTAlthough dynamics of the complex microbial ecosystem populating the gastrointestinal tract of animals has profound and multifaceted impacts on host’s metabolism and health, it remains unclear whether it is the intrinsic or extrinsic factors that play a more dominant role in mediating variations in the composition of intestinal microbiota. To address this, two strikingly different diets were studied: a high-protein, low-fiber formula feed (FF), and low-protein, high-fiber Sudan grass (SG). After a 16-week feeding trial on a herbivorous fish, grass carp, microbial profiles of midgut (M) and hindgut (H) segments of both groups were compared. Bacteroidetes were more abundant in the hindgut (T=-7.246, p<0.001), and Proteobacteria in the midgut (T=4.383, p<0.001). Fusobacteria were more abundant in the FF group (compared to the SG group, T=2.927, p<0.001). Bacterial composition was different (p<0.05) between the midguts of formula feed (M-FF) and Sudan grass (M-SG) groups, but not between the hindguts of two groups (H-FF and H-SG; p=0.269). PerMANOVA and VPA indicated that the gut segment contributed 19.8% (p<0.001) and 28% (p<0.001) of the variation of microbial communities, whereas diet contributed only 8.0% (p<0.001) and 14% (p<0.001), respectively. Overall, results suggest that intestinal compartments are a stronger determinant than diet in shaping the intestinal microbiota. Specifically, whereas diet has a strong impact on the microbiome composition in proximal gut compartments, this impact is much less pronounced distally, which is likely to be a reflection of a limited ability of some microbial taxa to thrive in the anoxic environment in distal segments.IMPORTANCEThe impact of compositional dynamics of gut microbiota on host’s metabolism and health is so profound that the traditional idea of biological individual is increasingly replaced with "holobiont", comprising both the host and its microbiome. Composition of gut microbiota is strongly influenced by extrinsic (such as diet) and intrinsic (such as gut compartment) factors. Despite ample scientific attention both of these factors have received individually, their relative contributions in mediating the dynamics of the microbiome remain unknown. Given the importance of this issue, we set out to disentangle their individual contributions in a herbivorous fish, grass carp. We found that intestinal compartments are a stronger determinant than diet in shaping the intestinal microbiota. Whereas the impact of diet is strongly pronounced in proximal gut compartments, it appears that limited ability of some microbial taxa to thrive in the anoxic environment in distal segments strongly reduces the impact of diet distally.

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Microbial Interactions and Roles in Soil Fertility in Seasonal Freeze-Thaw Periods under Different Straw Returning Strategies

Agriculture ◽

10.3390/agriculture11080779 ◽

2021 ◽

Vol 11 (8) ◽

pp. 779

Author(s):

Mengqi Sun ◽

Baoyu Chen ◽

Hongjun Wang ◽

Nan Wang ◽

Taigang Ma ◽

...

Keyword(s):

Community Structure ◽

Soil Fertility ◽

Bacterial Communities ◽

Freeze Thaw ◽

Soil Bacterial Communities ◽

Straw Return ◽

Bacteria Community Structure ◽

Thaw Period ◽

The Relationship ◽

Bacterial Groups

With the increase of world food demand, the intensity of cultivated land use also increased. To improve soil nutrient concentrations and crop yield, several straw returning techniques have been developed. Studies have shown that straw returning is beneficial to soil, but few studies have focused on the relationship between microbes and fertility in seasonal freeze-thaw periods. A two-year cropland experiment was set up that comprised three different straw return strategies, namely covering tillage with straw return for two years (CS), rotary tillage and straw return for two years (RS), rotary covering tillage with straw return (first year covering and the second year rotary tillage) (CRS), and conventional tillage with no straw return (CK). Illumina Miseq high throughput sequencing of 16S rRNA was applied to assess bacteria community structure. The relationship between bacteria community structure and changes in soil fertility induced by different straw incorporating during seasonal trends was studied. Our results showed that soil bacterial communities varied significantly during the soil seasonal freeze-thaw period in the northwest of Jilin province, China, and were influenced, to some extent, by the different straw returning procedures. Multidimensional analysis revealed that total phosphorus (TP), available nitrogen (AN), and total nitrogen (TN) were the major drivers of bacterial community structure. The co-occurrence network was divided into several modules. Notably, the major bacterial modules varied significantly in different sampling periods and different treatments. These results suggested that specific bacterial groups could contribute to soil fertility in relation to environmental fluctuations. Some bacterial groups (e.g., Pyrinomonadales, Rhizobiales, Sphingomonadales, and Xanthomonadales, in order level) were directly linked with specific environmental factors, indicating the key roles of these groups in soil fertility. In summary, the soil bacterial communities varied significantly during the freeze-thaw period and might play important roles in the degradation of straw. Thus, the straw return could enhance soil fertility.

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Microhabitats are associated with diversity–productivity relationships in freshwater bacterial communities

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa029 ◽

2020 ◽

Vol 96 (4) ◽

Cited By ~ 2

Author(s):

Marian L Schmidt ◽

Bopaiah A Biddanda ◽

Anthony D Weinke ◽

Edna Chiang ◽

Fallon Januska ◽

...

Keyword(s):

Bacterial Communities ◽

Habitat Heterogeneity ◽

Positive Relationship ◽

Effective Number ◽

Free Living ◽

Associated Production ◽

Biodiversity And Ecosystem Function ◽

Bacterial Richness ◽

The Impact ◽

The Relationship

ABSTRACT Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.

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Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status

Applied and Environmental Microbiology ◽

10.1128/aem.66.1.345-351.2000 ◽

2000 ◽

Vol 66 (1) ◽

pp. 345-351 ◽

Cited By ~ 347

Author(s):

Ching-Hong Yang ◽

David E. Crowley

Keyword(s):

Community Structure ◽

Nutritional Status ◽

Microbial Communities ◽

16S Rdna ◽

Bacterial Communities ◽

Root Exudate ◽

Primary Root ◽

Root Tips ◽

Root Zones ◽

The Impact

ABSTRACT Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.

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Microhabitats shape diversity-productivity relationships in freshwater bacterial communities

10.1101/231688 ◽

2017 ◽

Author(s):

Marian L. Schmidt ◽

Bopaiah A. Biddanda ◽

Anthony D. Weinke ◽

Edna Chiang ◽

Fallon Januska ◽

...

Keyword(s):

Bacterial Communities ◽

Phylogenetic Diversity ◽

Community Diversity ◽

Bacterial Productivity ◽

Free Living ◽

Biodiversity And Ecosystem Function ◽

Per Capita ◽

The Impact ◽

The Relationship ◽

Heterotrophic Production

AbstractEukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on richness, evenness, or phylogenetic diversity, and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake. Diversity measures, and not environmental variables, were the best predictors of particle-associated heterotrophic production. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened with evenness. There were no observable BEF trends in free-living bacterial communities. Across both habitats, communities with more phylogenetically related taxa had higher per-capita heterotrophic production than communities of phylogenetically distantly related taxa. Our findings show that heterotrophic bacterial productivity is positively correlated with evenness and richness, negatively with phylogenetic diversity, and that BEF relationships are contingent on microhabitats. Our work adds to the understanding of the highly distinct contributions to community diversity and ecosystem functioning contributed by bacteria in free-living and particle-associated aquatic habitats.

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Biofilm Bacterial Community Structure in Streams Affected by Acid Mine Drainage

Applied and Environmental Microbiology ◽

10.1128/aem.00274-09 ◽

2009 ◽

Vol 75 (11) ◽

pp. 3455-3460 ◽

Cited By ~ 55

Author(s):

Gavin Lear ◽

Dev Niyogi ◽

Jon Harding ◽

Yimin Dong ◽

Gillian Lewis

Keyword(s):

Community Structure ◽

Acid Mine Drainage ◽

Bacterial Community ◽

Bacterial Communities ◽

Mine Drainage ◽

Iron Hydroxide ◽

Acidic Ph ◽

Dissolved Metals ◽

Acid Mine ◽

The Impact

ABSTRACT We examined the bacterial communities of epilithic biofilms in 17 streams which represented a gradient ranging from relatively pristine streams to streams highly impacted by acid mine drainage (AMD). A combination of automated ribosomal intergenic spacer analysis with multivariate analysis and ordination provided a sensitive, high-throughput method to monitor the impact of AMD on stream bacterial communities. Significant differences in community structure were detected among neutral to alkaline (pH 6.7 to 8.3), acidic (pH 3.9 to 5.7), and very acidic (pH 2.8 to 3.5) streams. DNA sequence analysis revealed that the acidic streams were generally dominated by bacteria related to the iron-oxidizing genus Gallionella, while the organisms in very acidic streams were less diverse and included a high proportion of acidophilic eukaryotes, including taxa related to the algal genera Navicula and Klebsormidium. Despite the presence of high concentrations of dissolved metals (e.g., Al and Zn) and deposits of iron hydroxide in some of the streams studied, pH was the most important determinant of the observed differences in bacterial community variability. These findings confirm that any restoration activities in such systems must focus on dealing with pH as the first priority.

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