Dietary Patterns and Associated Microbiome Changes that Promote Oncogenesis

The recent increases in cancer incidences have been linked to lifestyle changes that result in obesity and metabolic syndrome. It is now evident that these trends are associated with the profound changes that occur in the intestinal microbiome, producing altered microbial population signatures that interact, directly or indirectly, with potentially pro-carcinogenic molecular pathways of transcription, proliferation, and inflammation. The effects of the entire gut microbial population on overall health are complex, but individual bacteria are known to play important and definable roles. Recent detailed examinations of a large number of subjects show a tight correlation between habitual diets, fecal microbiome signatures, and markers of metabolic health. Diets that score higher in healthfulness or diversity such as plant-based diets, have altered ratios of specific bacteria, including an increase in short-chain fatty acid producers, which in turn have been linked to improved metabolic markers and lowered cancer risk. Contrarily, numerous studies have implicated less healthy, lower-scoring diets such as the Western diet with reduced intestinal epithelial defenses and promotion of specific bacteria that affect carcinogenic pathways. In this review, we will describe how different dietary patterns affect microbial populations in the gut and illustrate the subsequent impact of bacterial products and metabolites on molecular pathways of cancer development, both locally in the gut and systemically in distant organs.

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Linking Toluene Degradation with Specific Microbial Populations in Soil

Applied and Environmental Microbiology ◽

10.1128/aem.65.12.5403-5408.1999 ◽

1999 ◽

Vol 65 (12) ◽

pp. 5403-5408 ◽

Cited By ~ 72

Author(s):

Jessica R. Hanson ◽

Jennifer L. Macalady ◽

David Harris ◽

Kate M. Scow

Keyword(s):

Microbial Community ◽

Microbial Population ◽

Phospholipid Fatty Acid ◽

Microbial Populations ◽

Complex Environments ◽

Toluene Degradation ◽

Effective Technique ◽

Soil Microbial ◽

Isotope Tracer ◽

Plfa Analysis

ABSTRACT Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil.

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Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

mSystems ◽

10.1128/msystems.00367-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Ganesh Babu Malli Mohan ◽

Ceth W. Parker ◽

Camilla Urbaniak ◽

Nitin K. Singh ◽

Anthony Hood ◽

...

Keyword(s):

16S Rrna ◽

Metal Surfaces ◽

Microbial Population ◽

Microbial Populations ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Particle Board ◽

Shotgun Metagenomics ◽

Glass Surfaces ◽

Glass Metal

ABSTRACT Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance. IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.

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Dietary Patterns Differentially Affect Microbiome Composition and Function in a Porcine Model of Obesity-related Metabolic Disorder (OR23-04-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz040.or23-04-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Gloria Solano-Aguilar ◽

Jonathan Shao ◽

Joseph Urban ◽

Sukla Lakshman ◽

Saebyeol Jang ◽

...

Keyword(s):

Dietary Patterns ◽

Dietary Intervention ◽

Diversity Index ◽

Early Stage ◽

Saturated Fat ◽

Post Intervention ◽

Fecal Microbiome ◽

Microbiome Composition ◽

And Function ◽

The Impact

Abstract Objectives To determine the impact of two isocaloric diets containing (38% ,15% and 47% energy from fat, protein and carbohydrate, respectively): Western diet (WD) rich in saturated fat, refined carbohydrate, low in fiber and high in cholesterol, and a heart healthy diet (HHD) rich in unsaturated fat, unrefined carbohydrate, fruits/vegetables, high in fiber and low in cholesterol, on the composition and function of the gut microbiome Methods Thirty-Ossabaw pigs were fed WD or HHD diets with half within each group therapeutically treated with statin (atorvastatin [Lipitor]). The fecal microbiome was analyzed one and six months after dietary intervention by 16S rRNA sequencing and metagenomic function was empirically inferred Results Genus diversity was transiently affected with a reduced Shannon Diversity index one month after feeding the WD or HHD (FDR P < 0.05) with no change between groups at 6 months. Bacterial communities were clustered and separated by diet independent of gender and separated by treatment with statin in the HHD only. Verrucomicrobiaceae (Akkermansia) and Methanobacteriales (Methanobrevibacter) were increased in pigs as early as one month after feeding the HHD, as was Clostridiales and Bifidobacterium (associated with optimal intestinal health). There was an enrichment of Proteobacteria (Succinivibrionaceae, Desulfovibrionaceae) in pigs fed the WD. Additional members of the Firmicutes phylum were detected. Diet-dependent associations (all P < 0.05) were identified between Lachnospiraceae members and early host dyslipidemia, inflammation, and atheromatous lesions in the left anterior descending proximal (LAD) and LAD/Left circumflex (LCX) bifurcation six months post-intervention. Conclusions These data document for the first time a distinctive bacterial profile in Ossabaw pigs with a diet-induced dyslipidemia and early stage atherosclerosis. Taken together these results represent a new model to examine mechanistic pathways of dietary patterns and/or drug interactions and its effect on modulating microbiome in developing atherosclerosis. Funding Sources USDA project 8040-51530-056-00 and Inter Agency USDA Agreement 588-1950-9-001 between BHNRC and Jean Mayer USDA-HNRCA

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A Review on Anaerobic Co-Digestion with a Focus on the Microbial Populations and the Effect of Multi-Stage Digester Configuration

Energies ◽

10.3390/en12061106 ◽

2019 ◽

Vol 12 (6) ◽

pp. 1106 ◽

Cited By ~ 50

Author(s):

Anahita Rabii ◽

Saad Aldin ◽

Yaser Dahman ◽

Elsayed Elbeshbishy

Keyword(s):

Anaerobic Digestion ◽

Microbial Population ◽

System Stability ◽

Microbial Consortia ◽

Microbial Populations ◽

Stage Versus ◽

Two Stage ◽

Waste Sludge ◽

Multi Stage ◽

Mode A

Recent studies have shown that anaerobic co-digestion (AnCoD) is superior to conventional anaerobic digestion (AD). The benefits of enhanced bioenergy production and solids reduction using co-substrates have attracted researchers to study the co-digestion technology and to better understand the effect of multi substrates on digester performance. This review will discuss the results of such studies with the main focus on: (1) generally the advantages of co-digestion over mono-digestion in terms of system stability, bioenergy, and solids reduction; (2) microbial consortia diversity and their synergistic impact on biogas improvement; (3) the effect of digester mode, i.e., multi-stage versus single stage digestion on AnCoD. It is essential to note that the studies reported improvement in the synergy and diverse microbial consortia when using co-digestion technologies, in addition to higher biomethane yield when using two-stage mode. A good example would be the co-digestion of biodiesel waste and glycerin with municipal waste sludge in a two-stage reactor resulting in 100% increase of biogas and 120% increase in the methane content of the produced biogas with microbial population dominated by Methanosaeta and Methanomicrobium.

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Molecular Analysis of Surfactant-Driven Microbial Population Shifts in Hydrocarbon-Contaminated Soil

Applied and Environmental Microbiology ◽

10.1128/aem.66.7.2959-2964.2000 ◽

2000 ◽

Vol 66 (7) ◽

pp. 2959-2964 ◽

Cited By ~ 65

Author(s):

Gregory M. Colores ◽

Richard E. Macur ◽

David M. Ward ◽

William P. Inskeep

Keyword(s):

Gel Electrophoresis ◽

Microbial Population ◽

Denaturing Gradient Gel Electrophoresis ◽

Microbial Populations ◽

Alcohol Ethoxylate ◽

Rrna Gene ◽

Mineralization Kinetics ◽

Gradient Gel Electrophoresis ◽

The Impact ◽

Parallel Cultivation

ABSTRACT We analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. A mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. Witconol SN70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (CMC) in soil (CMC′) (determined to be 13 mg g−1). Addition of the surfactant at a concentration below the CMC′ (2 mg g−1) did not affect the mineralization rates of either hydrocarbon. However, when surfactant was added at a concentration approaching the CMC′ (10 mg g−1), hexadecane mineralization was delayed and phenanthrene mineralization was completely inhibited. Addition of surfactant at concentrations above the CMC′ (40 mg g−1) completely inhibited mineralization of both phenanthrene and hexadecane. Denaturing gradient gel electrophoresis of 16S rRNA gene segments showed that hydrocarbon amendment stimulatedRhodococcus and Nocardia populations that were displaced by Pseudomonas and Alcaligenespopulations at elevated surfactant levels. Parallel cultivation studies revealed that the Rhodococcus population can utilize hexadecane and that the Pseudomonas andAlcaligenes populations can utilize both Witconol SN70 and hexadecane for growth. The results suggest that surfactant applications necessary to achieve the CMC alter the microbial populations responsible for hydrocarbon mineralization.

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Soil bulk density effects on soil microbial populations and enzyme activities during the growth of maize (Zea mays L.) planted in large pots under field exposure

Canadian Journal of Soil Science ◽

10.4141/s01-026 ◽

2002 ◽

Vol 82 (2) ◽

pp. 147-154 ◽

Cited By ~ 37

Author(s):

C. H. Li ◽

B. L. Ma ◽

T. Q. Zhang

Keyword(s):

Zea Mays ◽

Bulk Density ◽

Enzyme Activities ◽

Soil Compaction ◽

Microbial Population ◽

Soil Bulk Density ◽

Microbial Populations ◽

Growth Stages ◽

Soil Microbial ◽

Plant Growth Stages

Soil compaction associated with inappropriate maneuvering of field equipment, and/or modern cropping system negatively affect soil physical properties, and thus, may limit microbial activities and biochemical processes, which are important to nutrient bioavailability. An experiment was carried out using the pot-culture technique to determine the effect of bulk density on soil microbial populations and enzyme activities in an Eutric Cambisol sandy loam soil (United Nations’ classification) planted with maize (Zea mays L.) in the Experimental Farm of Henan Agricultural University, Henan, China (34°49′N, 113°40′E). Numbers of bacteria, fungi, and actinomycetes and the enzyme activities of invertase, polyphenol oxidase, catalase, urease, protease, and phosphatase were determined at various stages during the plant growing season. Microbial numbers were negatively and linearly related to soil bulk density. With increases in soil bulk density from 1.00 to 1.60 Mg m-3, total numbers of bacteria, fungi and actinomycetes declined by 26-39%. The strongest correlations between the soil microbial population and bulk density occurred at the plant growth stages of the 6 fully expanded leaf (V6) and anthesis (R1), with R2 > 0.90 (P< 0.01) for all three microorganism categories. Increasing soil bulk density was related quadratically to the activities of soil invertase and polyphenol oxidase, protease and catalase. It appears that the greatest activities of most soil enzymes occurred at a bulk density of 1.0 to 1.3 Mg m-3, which are optimum for most field crops. The plant growth stages also had an important impact on soil enzyme activities and microbial populations, with strong positive associations between soil microorganisms and enzyme activities with crop growth. Key words: Maize, soil enzymes, microbial population, soil compaction, bulk density, Zea mays

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Redox regime shifts in microbially mediated biogeochemical cycles

Biogeosciences ◽

10.5194/bg-12-3713-2015 ◽

2015 ◽

Vol 12 (12) ◽

pp. 3713-3724 ◽

Cited By ~ 4

Author(s):

T. Bush ◽

I. B. Butler ◽

A. Free ◽

R. J. Allen

Keyword(s):

Population Dynamics ◽

Environmental Change ◽

Microbial Population ◽

Biogeochemical Cycles ◽

Sulfur Cycle ◽

Regime Shifts ◽

Microbial Populations ◽

Iron Cycling ◽

Biogeochemical Models ◽

Microbial Population Dynamics

Abstract. Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet they are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the present-day sulfur cycle in the natural environment and the present-day nitrogen cycle in eutrophic terrestrial environments. These shifts may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

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Mikrobiom und gastrointestinale Erkrankungen

DMW - Deutsche Medizinische Wochenschrift ◽

10.1055/a-0899-8759 ◽

2019 ◽

Vol 144 (14) ◽

pp. 949-956

Author(s):

Julian Siegel ◽

Viola Andresen ◽

Peter Layer

Keyword(s):

Gastrointestinal Diseases ◽

Intestinal Microbiome ◽

Therapeutic Approaches ◽

Fecal Microbiome ◽

Gastrointestinale Erkrankungen ◽

Microbiome Research ◽

Long Time ◽

Inflammatory Bowel ◽

Complex Relationships ◽

Pathogenic Agents

AbstractFor some years, microbiome research has become a thriving topic. The most diverse and hitherto poorly understood connections of interactions of the microbiome with the host body (human) seem to play an important role in the genesis of a wide variety of diseases. This article focuses on the importance of the microbiome in gastrointestinal diseases and presents therapeutic approaches.The intestinal microbiome will not be understood completely for a long time due to the highly complex relationships and variety of different microorganisms. The intestinal microbiome is critically involved in the development of diseases, especially in the development of inflammatory bowel disease. Helicobacter pylori infection is a major risk factor for gastric carcinoma. Esophageal microbiome alterations can cause inflammation and decrease the tone of the lower esophageal sphincter. Inflammation is a crucial pathway for tumorigenesis, it can be caused by the “normal” flora and by pathogenic agents. In the microbiome of the colon, interactions of bacteria, viruses and fungi have a very special status. Good oral/dental status protects against pancreatic carcinoma. Fecal microbiome transfer has become more important in the American guideline. Understanding the processes in the intestinal microbiome provides approaches to new therapies that are likely to exceed our current imagination.

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In‐situ apparent conductivity measurements and microbial population distribution at a hydrocarbon‐contaminated site

Geophysics ◽

10.1190/1.1649375 ◽

2004 ◽

Vol 69 (1) ◽

pp. 56-63 ◽

Cited By ~ 64

Author(s):

Estella A. Atekwana ◽

D. Dale Werkema ◽

Joseph W. Duris ◽

Silvia Rossbach ◽

Eliot A. Atekwana ◽

...

Keyword(s):

Microbial Degradation ◽

Microbial Population ◽

Population Distribution ◽

Microbial Populations ◽

Contaminated Site ◽

Most Probable Number ◽

Bulk Conductivity ◽

Probable Number ◽

A Site

We investigated the bulk electrical conductivity and microbial population distribution in sediments at a site contaminated with light nonaqueous‐phase liquid (LNAPL). The bulk conductivity was measured using in‐situ vertical resistivity probes; the most probable number method was used to characterize the spatial distribution of aerobic heterotrophic and oil‐degrading microbial populations. The purpose of this study was to assess if high conductivity observed at aged LNAPL‐impacted sites may be related to microbial degradation of LNAPL. The results show higher bulk conductivity coincident with LNAPL‐impacted zones, in contrast to geoelectrical models that predict lower conductivity in such zones. The highest bulk conductivity was observed to be associated with zones impacted by residual and free LNAPL. Data from bacteria enumeration from sediments close to the resistivity probes show that oil‐degrading microbes make up a larger percentage (5–55%) of the heterotrophic microbial community at depths coincident with the higher conductivity compared to ∼5% at the uncontaminated location. The coincidence of a higher percentage of oil‐degrading microbial populations in zones of higher bulk conductivity suggests that the higher conductivity in these zones may result from increased fluid conductivity related to microbial degradation of LNAPL, consistent with geochemical studies that suggest that intrinsic biodegradation is occurring at the site. The findings from this study point to the fact that biogeochemical processes accompanying biodegradation of contaminants can potentially alter geoelectrical properties of the subsurface impacted media.

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Redox regime shifts in microbially-mediated biogeochemical cycles

Biogeosciences Discussions ◽

10.5194/bgd-12-3283-2015 ◽

2015 ◽

Vol 12 (4) ◽

pp. 3283-3314

Author(s):

T. Bush ◽

I. B. Butler ◽

A. Free ◽

R. J. Allen

Keyword(s):

Population Dynamics ◽

Environmental Change ◽

Microbial Population ◽

Biogeochemical Cycles ◽

Regime Shifts ◽

Microbial Populations ◽

Iron Cycling ◽

Biogeochemical Models ◽

Microbial Population Dynamics ◽

Parameter Ranges

Abstract. Understanding how the Earth's biogeochemical cycles respond to environmental change is a prerequisite for the prediction and mitigation of the effects of anthropogenic perturbations. Microbial populations mediate key steps in these cycles, yet are often crudely represented in biogeochemical models. Here, we show that microbial population dynamics can qualitatively affect the response of biogeochemical cycles to environmental change. Using simple and generic mathematical models, we find that nutrient limitations on microbial population growth can lead to regime shifts, in which the redox state of a biogeochemical cycle changes dramatically as the availability of a redox-controlling species, such as oxygen or acetate, crosses a threshold (a "tipping point"). These redox regime shifts occur in parameter ranges that are relevant to the sulfur and nitrogen cycles in the present-day natural environment, and may also have relevance to iron cycling in the iron-containing Proterozoic and Archean oceans. We show that redox regime shifts also occur in models with physically realistic modifications, such as additional terms, chemical states, or microbial populations. Our work reveals a possible new mechanism by which regime shifts can occur in nutrient-cycling ecosystems and biogeochemical cycles, and highlights the importance of considering microbial population dynamics in models of biogeochemical cycles.

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