Cohort Specific Effects of Cereal-bar Supplementation in Overweight Patients With or Without Type 2 Diabetes Mellitus

AbstractThe importance of gut microbes to metabolic health is becoming more evident and nutrition-based therapies to alter the composition of bacterial communities to manage metabolic disease are an attractive avenue to ameliorate some effects of Western diets. While the composition of gut microbial communities can vary significantly across disease states, it is not well known if these communities have common responses to nutritional interventions. To better understand fiber-bacterial community interactions, we collected biological parameters and fecal samples of overweight non-diabetic (OND) and diabetic (OD) individuals before and after daily supplementation of 2.8 g β-glucan on their habitual diet for 30 days. Fecal bacterial communities in an age-matched cohort were measured by sequencing partial 16S rRNA genes and imputed metagenomic content. Unexpectedly, we observed disconnected responses of biological measurements and the bacterial community. Based on average effect size, biological measurements were greater in the OND group while effects on the bacterial community were greatest on the OD cohort, and we suspect these observations are due to the significantly lower alpha diversity in the OD cohort. Our data indicate that responses to fiber supplementation are cohort specific and this should be considered when manipulating the microbiome via fiber supplementation.

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Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

Frontiers in Microbiology ◽

10.3389/fmicb.2021.783563 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wen Luo ◽

Xiaoyu Zai ◽

Jieyu Sun ◽

Da Li ◽

Yuanli Li ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Bacterial Communities ◽

Plant Root ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Root Diameter ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rooting Depth

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

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Rhizosphere Community Selection Reveals Bacteria Associated With Reduced Root Disease

10.21203/rs.3.rs-64051/v1 ◽

2020 ◽

Author(s):

Chuntao Yin ◽

Juan M. Casa Vargas ◽

Daniel C. Schlatter ◽

Christina H. Hagerty ◽

Scot H. Hulbert ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Microbial Communities ◽

Bacterial Communities ◽

Wheat Root ◽

Root Disease ◽

Plant Diseases ◽

16S Rrna Genes ◽

Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

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The Effect of a Sublethal Temperature Elevation on the Structure of Bacterial Communities Associated with the CoralPorites compressa

Journal of Marine Biology ◽

10.1155/2011/969173 ◽

2011 ◽

Vol 2011 ◽

pp. 1-9 ◽

Cited By ~ 6

Author(s):

Jennifer L. Salerno ◽

Dan R. Reineman ◽

Ruth D. Gates ◽

Michael S. Rappé

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

16S Rrna Genes ◽

Rrna Genes ◽

Polymorphism Analysis ◽

Significant Shift ◽

Coral Host ◽

Experimental Conditions

Evidence points to a link between environmental stressors, coral-associated bacteria, and coral disease; however, few studies have examined the details of this relationship under tightly controlled experimental conditions. To address this gap, an array of closed-system, precision-controlled experimental aquaria were used to investigate the effects of an abrupt 1°C above summer ambient temperature increase on the bacterial community structure and photophysiology ofPorites compressacorals. While the temperature treatment rapidly impacted the photophysiology of the coral host, it did not elicit a statistically significant shift in bacterial community structure from control, untreated corals as determined by terminal restriction fragment length polymorphism analysis of 16S rRNA genes. Two of three coral colonies harbored more closely related bacterial communities at the time of collection and, despite statistically significant shifts in bacterial community structure for both control and treatment corals during the 10-day acclimation period, maintained this relationship over the course of the experiment. The experimental design used in this study proved to be a robust, reproducible system for investigating coral microbiology in an aquarium setting.

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Axial Dynamics, Stability, and Interspecies Similarity of Bacterial Community Structure in the Highly Compartmentalized Gut of Soil-Feeding Termites (Cubitermes spp.)

Applied and Environmental Microbiology ◽

10.1128/aem.69.10.6018-6024.2003 ◽

2003 ◽

Vol 69 (10) ◽

pp. 6018-6024 ◽

Cited By ~ 65

Author(s):

Dirk Schmitt-Wagner ◽

Michael W. Friedrich ◽

Bianca Wagner ◽

Andreas Brune

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Rflp Analysis ◽

Companion Paper ◽

16S Rrna Genes ◽

Rrna Genes ◽

Molecular Fingerprints ◽

Physicochemical Conditions

ABSTRACT The highly compartmentalized gut of soil-feeding termites is characterized by pronounced axial dynamics in physicochemical conditions and microbial processes. In a companion paper (D. Schmitt-Wagner, M. W. Friedrich, B. Wagner, and A. Brune, Appl. Environ. Microbiol. 69:6007-6017, 2003), we demonstrated that the variety of physicochemical conditions in the different gut compartments of Cubitermes spp. is reflected in the diversity of the respective intestinal microbial communities. Here, we used molecular fingerprints of 16S rRNA genes of the bacterial community, obtained by terminal restriction fragment length polymorphism (T-RFLP) analysis, to describe the axial dynamics of the bacterial community structure in the different gut sections. Comparison of the T-RFLP profiles with the predicted terminal restriction fragments of the clones in clone libraries of the gut segments in Cubitermes orthognathus confirmed that all hindgut sections harbored distinct bacterial communities. Morisita indices of community similarity, calculated by comparing the different patterns, revealed large differences between the bacterial communities of soil, gut, and nest material and also among the individual gut sections. By contrast, comparison of the homologous gut segments of different Cubitermes species indicated that the three termite species investigated possessed a similar, gut-specific microbiota that remained comparatively stable even during several months of maintenance in the laboratory.

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Rhizosphere community selection reveals bacteria associated with reduced root disease

Microbiome ◽

10.1186/s40168-020-00997-5 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Chuntao Yin ◽

Juan M. Casa Vargas ◽

Daniel C. Schlatter ◽

Christina H. Hagerty ◽

Scot H. Hulbert ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Microbial Communities ◽

Bacterial Communities ◽

Wheat Root ◽

Root Disease ◽

Plant Diseases ◽

16S Rrna Genes ◽

Rrna Genes

Abstract Background Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

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Robust Hydrocarbon Degradation and Dynamics of Bacterial Communities during Nutrient-Enhanced Oil Spill Bioremediation

Applied and Environmental Microbiology ◽

10.1128/aem.68.11.5537-5548.2002 ◽

2002 ◽

Vol 68 (11) ◽

pp. 5537-5548 ◽

Cited By ~ 321

Author(s):

Wilfred F. M. Röling ◽

Michael G. Milner ◽

D. Martin Jones ◽

Kenneth Lee ◽

Fabien Daniel ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Oil Spill ◽

Bacterial Communities ◽

Inorganic Nutrients ◽

16S Rrna Genes ◽

Rrna Genes ◽

Oil Degradation ◽

Beach Sediment ◽

Wide Range

ABSTRACT Degradation of oil on beaches is, in general, limited by the supply of inorganic nutrients. In order to obtain a more systematic understanding of the effects of nutrient addition on oil spill bioremediation, beach sediment microcosms contaminated with oil were treated with different levels of inorganic nutrients. Oil biodegradation was assessed respirometrically and on the basis of changes in oil composition. Bacterial communities were compared by numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified 16S rRNA genes and cloning and sequencing of PCR-amplified 16S rRNA genes. Nutrient amendment over a wide range of concentrations significantly improved oil degradation, confirming that N and P limited degradation over the concentration range tested. However, the extent and rate of oil degradation were similar for all microcosms, indicating that, in this experiment, it was the addition of inorganic nutrients rather than the precise amount that was most important operationally. Very different microbial communities were selected in all of the microcosms. Similarities between DGGE profiles of replicate samples from a single microcosm were high (95% ± 5%), but similarities between DGGE profiles from replicate microcosms receiving the same level of inorganic nutrients (68% ± 5%) were not significantly higher than those between microcosms subjected to different nutrient amendments (63% ± 7%). Therefore, it is apparent that the different communities selected cannot be attributed to the level of inorganic nutrients present in different microcosms. Bioremediation treatments dramatically reduced the diversity of the bacterial community. The decrease in diversity could be accounted for by a strong selection for bacteria belonging to the alkane-degrading Alcanivorax/Fundibacter group. On the basis of Shannon-Weaver indices, rapid recovery of the bacterial community diversity to preoiling levels of diversity occurred. However, although the overall diversity was similar, there were considerable qualitative differences in the community structure before and after the bioremediation treatments.

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Changes in the Soil Bacterial Community in a Chronosequence of Temperate Walnut-Based Intercropping Systems

Forests ◽

10.3390/f10040299 ◽

2019 ◽

Vol 10 (4) ◽

pp. 299 ◽

Cited By ~ 3

Author(s):

Pengxiang Gao ◽

Xiaofeng Zheng ◽

Lai Wang ◽

Bin Liu ◽

Shuoxin Zhang

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Agroforestry System ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Phyla ◽

Soil Bacterial Communities ◽

Soil Bacterial

Agroforestry (tree-based intercropping) is regarded as a promising practice in sustainable agricultural management. However, the impacts of converting cropland to an agroforestry system on microbial communities remain poorly understood. In this study, we assessed the soil bacterial communities in conventional wheat monoculture systems and a chronosequence (5–14 years) walnut-wheat agroforestry system through the high-throughput sequencing of 16S rRNA genes to investigate the effect of agroforestry age on soil bacterial communities and the correlation between soil properties and bacterial communities in the agroecosystem. Our results demonstrate that establishing and developing walnut tree-based agroforestry increased soil bacterial diversity and changed bacterial community structure. Firmicutes, Proteobacteria, Actinobacteria and Acidobacteria were the dominant soil bacterial phyla and Bacillus was the dominant genus. Crop monoculture systems were characterized by the Bacillus (Firmicutes)-dominated microbial community. The relative abundance of Bacillus decreased with agroforestry age; however, subgroups of Proteobacteria and Actinobacteria increased. Of the selected soil physicochemical properties, soil pH and bulk density were significantly correlated with bacterial alpha diversity, and soil pH and organic carbon were the principal drivers in shaping the soil microbial structure as revealed by redundancy analysis (RDA).

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Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6784-6792.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6784-6792 ◽

Cited By ~ 114

Author(s):

Naoise Nunan ◽

Timothy J. Daniell ◽

Brajesh K. Singh ◽

Artemis Papert ◽

James W. McNicol ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

Bacterial Community Composition ◽

Molecular Techniques ◽

16S Rrna Genes ◽

Rrna Genes ◽

Grassland Soils

ABSTRACT Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.

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Comparison of Soil Bacterial Communities in Rhizospheres of Three Plant Species and the Interspaces in an Arid Grassland

Applied and Environmental Microbiology ◽

10.1128/aem.68.4.1854-1863.2002 ◽

2002 ◽

Vol 68 (4) ◽

pp. 1854-1863 ◽

Cited By ~ 233

Author(s):

Cheryl R. Kuske ◽

Lawrence O. Ticknor ◽

Mark E. Miller ◽

John M. Dunbar ◽

Jody A. Davis ◽

...

Keyword(s):

Bacterial Community ◽

Plant Species ◽

Environmental Conditions ◽

Bacterial Communities ◽

Soil Depth ◽

Plant Cover ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Dna ◽

Total Bacterial Community

ABSTRACT Soil bacteria are important contributors to primary productivity and nutrient cycling in arid land ecosystems, and their populations may be greatly affected by changes in environmental conditions. In parallel studies, the composition of the total bacterial community and of members of the Acidobacterium division were assessed in arid grassland soils using terminal restriction fragment length polymorphism (TRF, also known as T-RFLP) analysis of 16S rRNA genes amplified from soil DNA. Bacterial communities associated with the rhizospheres of the native bunchgrasses Stipa hymenoides and Hilaria jamesii, the invading annual grass Bromus tectorum, and the interspaces colonized by cyanobacterial soil crusts were compared at three depths. When used in a replicated field-scale study, TRF analysis was useful for identifying broad-scale, consistent differences in the bacterial communities in different soil locations, over the natural microscale heterogeneity of the soil. The compositions of the total bacterial community and Acidobacterium division in the soil crust interspaces were significantly different from those of the plant rhizospheres. Major differences were also observed in the rhizospheres of the three plant species and were most apparent with analysis of the Acidobacterium division. The total bacterial community and the Acidobacterium division bacteria were affected by soil depth in both the interspaces and plant rhizospheres. This study provides a baseline for monitoring bacterial community structure and dynamics with changes in plant cover and environmental conditions in the arid grasslands.

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Rhizosphere community selection reveals bacteria associated with reduced root disease

10.21203/rs.3.rs-64051/v3 ◽

2020 ◽

Author(s):

Chuntao Yin ◽

Juan M. Casa Vargas ◽

Daniel C. Schlatter ◽

Christina H. Hagerty ◽

Scot H. Hulbert ◽

...

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Microbial Communities ◽

Bacterial Communities ◽

Wheat Root ◽

Root Disease ◽

Plant Diseases ◽

16S Rrna Genes ◽

Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities.Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil.Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

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