scholarly journals Disentangling race, environment and the microbiome in a study of preterm birth risk

2021 ◽  
Author(s):  
Shan Sun ◽  
Myrna Serrano ◽  
Jennifer Fettweis ◽  
Patricia Basta ◽  
Emma Rosen ◽  
...  
Keyword(s):  
Community Structure ◽  
Preterm Birth ◽  
Microbial Community ◽  
Black Women ◽  
Microbial Community Structure ◽  
White Women ◽  
Alpha Diversity ◽  
Term Birth ◽  
Lower Abundance ◽  
Microbial Biomarkers

Abstract Previous studies have investigated the associations between the vaginal microbiome and preterm birth (PTB), with the aim of determining whether differences in community patterns meaningfully alter risk, and could therefore be the target of intervention. We report on vaginal microbial analysis on a subset of the Pregnancy, Infection, and Nutrition (PIN) Study, a prospectively enrolled cohort of women in central North Carolina between 1995-2001. We selected a nested case-control subset of this cohort, including 464 White women (375 term birth and 89 spontaneous PTB, sPTB) and 360 Black women (276 term birth and 84 sPTB). Microbial DNA was extracted from genital track swabs collected mid-pregnancy, and subjected to 16S rRNA taxonomic profiling. We found that microbial community structure is associated with race and sPTB, although the influence of race is stronger than the influence of sPTB. The microbiome of Black women has higher alpha-diversity, higher abundance of Lactobacillus iners and lower abundance of Lactobacillus crispatus. These differences were obscured once maternal douching behavior was considered—specifically, among women who douche, there were no significant differences in microbiome by race. The sPTB associated microbiome exhibited a lower abundance of L. crispatus, while alpha diversity and L. iners were not significantly different. Associations between the microbiome and sPTB were only significant in women who do not douche. While race was a strong predictor of microbial community structure, we also observed strong intercorrelations between a range of maternal factors, including poverty, education, marital status, age, douching and race, with microbiome effect sizes in the range of 1.8-5.2% in univariate models. Therefore, race may simply be a proxy for other socially driven factors that differentiate microbiome community structures. Future work will continue to refine reliable microbial biomarkers for preterm birth across diverse cohorts.

scholarly journals Fecal Microbial Diversity and Structure Are Associated with Diet Quality in the Multiethnic Cohort Adiposity Phenotype Study

2019 ◽  
Vol 149 (9) ◽  
pp. 1575-1584 ◽  
Author(s):  
Gertraud Maskarinec ◽  
Meredith A J Hullar ◽  
Kristine R Monroe ◽  
John A Shepherd ◽  
Jeani Hunt ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Healthy Eating ◽  
Diet Quality ◽  
Microbial Community Structure ◽  
Alpha Diversity ◽  
Clinic Visit ◽  
Healthy Eating Index ◽  
Dietary Index ◽  
Multiethnic Cohort

ABSTRACT Background Variation in gut microbial community structure is partly attributed to variations in diet. A priori dietary indexes capture diet quality and have been associated with chronic disease risk. Objectives The aim of this study was to examine the association of diet quality, as assessed by the Healthy Eating Index, Alternative Healthy Eating Index-2010, alternate Mediterranean Diet, and the Dietary Approaches to Stop Hypertension Trial, with measures of fecal microbial community structure assessed in the Adiposity Phenotype Study (APS), an ethnically diverse study population with varied food intakes. Methods Multiethnic Cohort Study members completed a validated quantitative food frequency questionnaire (QFFQ) at cohort entry (1993–1996) and, for the APS subset, at clinic visit (2013–2015), when they also provided a stool sample. DNA was extracted from stool, and the V1-V3 region of the 16S rRNA gene was amplified and sequenced. Dietary index scores were computed based on the QFFQ and an extensive nutritional database. Using linear regression adjusted for relevant covariates, we estimated associations of dietary quality with microbiome measures and computed adjusted mean values of microbial measures by tertiles of dietary index scores. Results The 858 men and 877 women of white, Japanese American, Latino, Native Hawaiian, and African American ancestry had a mean age of 69.2 years at stool collection. Alpha diversity according to the Shannon index increased by 1–2% across tertiles of all 4 diet indexes measured at clinic visit. The mean relative abundance of the phylum Actinobacteria was 13–19% lower with higher diet quality across all 4 indexes (difference between tertile 3 and tertile 1 divided by tertile 1). Of the 104 bacterial genera tested, 21 (primarily from the phylum Firmicutes) were positively associated with at least 1 index after Bonferroni adjustment. Conclusion Diet quality was strongly associated with fecal microbial alpha diversity and beta diversity and several genera previously associated with human health.

scholarly journals The role of macrobiota in structuring microbial communities along rocky shores

2014 ◽  
Author(s):  
Catherine A Pfister ◽  
Jack A Gilbert ◽  
Sean M Gibbons
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Rocky Shore ◽  
Alpha Diversity ◽  
Rocky Shores ◽  
Microbial Composition ◽  
Habitat Specificity ◽  
Microbial Habitat ◽  
Inert Surfaces

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

scholarly journals The role of macrobiota in structuring microbial communities along rocky shores

2014 ◽  
Author(s):  
Catherine A Pfister ◽  
Jack A Gilbert ◽  
Sean M Gibbons
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Rocky Shore ◽  
Alpha Diversity ◽  
Rocky Shores ◽  
Microbial Composition ◽  
Habitat Specificity ◽  
Microbial Habitat ◽  
Inert Surfaces

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

scholarly journals Effects of Freezing-Thawing on Microbial Community Structure in the Soil of Old Apple Orchards

HortScience ◽  
2021 ◽  
pp. 1-7
Author(s):  
Haiyan Wang ◽  
Rong Zhang ◽  
Weitao Jiang ◽  
Yunfei Mao ◽  
Xuesen Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Alpha Diversity ◽  
Apple Orchards ◽  
Soil Layers ◽  
Soil Microbial ◽  
Average Temperature ◽  
Abundance And Diversity ◽  
The Relationship

The study here aimed to investigate the effects of pre-winter ditching and freezing-thawing on soil microbial structure in different soil layers of old apple orchards. A total of 30 samples were obtained from 3 Nov. 2016 to 9 Mar. 2017. The relative abundance, alpha diversity, community structure of fungi, and the relationship between environmental factors and microbial community structure were analyzed, and the greenhouse experiments were used for further verification. Results showed that the number of actinomycete and total bacterial colonies decreased, whereas the number of fungi sustained decreased, resulting in a higher bacteria/fungi ratio. The percentage of Fusarium initially decreased, then later increased by 11.38%, 3.469%, 2.35%, 2.29%, and 3.09%. However, Fusarium levels were still 9% lower on 9 Mar. 2017 that on 3 Nov. 2016. Both the abundance and diversity of the community were higher in the upper soil than in the lower. The main environmental factor contributing to the percentage of Fusarium change was average temperature (AT), although highest temperature (HT) and water content (WC) also had an impact. The Malus hupehensis Rehd. seedlings growing in lower soil were more vigorous than that in upper soil. In sum, pre-winter ditching and freezing-thawing in old apple orchards can reduce the abundance percentage of harmful Fusarium and promote the growth of M. hupehensis Rehd. seedlings.

The First Use of Biofilm Microbial Community Structure as an Indicator of Impact of Two Dams on the Elwha River (Washington)

2009 ◽  
Vol 27 (4) ◽  
pp. 385-387
Author(s):  
W. D. Eaton ◽  
B. Wilmot ◽  
E. Epler ◽  
S. Mangiamelli ◽  
D. Barry
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Elwha River

scholarly journals Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

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