scholarly journals Variation in Human Milk Composition Is Related to Differences in Milk and Infant Fecal Microbial Communities

2021 ◽  
Vol 9 (6) ◽  
pp. 1153
Author(s):  
Ryan M. Pace ◽  
Janet E. Williams ◽  
Bianca Robertson ◽  
Kimberly A. Lackey ◽  
Courtney L. Meehan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Human Milk ◽  
Microbial Communities ◽  
Geographical Variation ◽  
Milk Composition ◽  
Published Data ◽  
Community Structures ◽  
Microbial Community Structures ◽  
Infant Feces ◽  
Human Milk Oligosaccharide

Previously published data from our group and others demonstrate that human milk oligosaccharide (HMOs), as well as milk and infant fecal microbial profiles, vary by geography. However, little is known about the geographical variation of other milk-borne factors, such as lactose and protein, as well as the associations among these factors and microbial community structures in milk and infant feces. Here, we characterized and contrasted concentrations of milk-borne lactose, protein, and HMOs, and examined their associations with milk and infant fecal microbiomes in samples collected in 11 geographically diverse sites. Although geographical site was strongly associated with milk and infant fecal microbiomes, both sample types assorted into a smaller number of community state types based on shared microbial profiles. Similar to HMOs, concentrations of lactose and protein also varied by geography. Concentrations of HMOs, lactose, and protein were associated with differences in the microbial community structures of milk and infant feces and in the abundance of specific taxa. Taken together, these data suggest that the composition of human milk, even when produced by relatively healthy women, differs based on geographical boundaries and that concentrations of HMOs, lactose, and protein in milk are related to variation in milk and infant fecal microbial communities.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

scholarly journals Introducing TreeClimber, a Test To Compare Microbial Community Structures

2006 ◽  
Vol 72 (4) ◽  
pp. 2379-2384 ◽  
Author(s):  
Patrick D. Schloss ◽  
Jo Handelsman
Keyword(s):  
Population Genetics ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Structures ◽  
New Methods ◽  
Microbial Community Structures ◽  
Ecological Complexity

ABSTRACT The phylogenetic and ecological complexity of microbial communities necessitates the development of new methods to determine whether two or more communities have the same structure even though it is not possible to sample the communities exhaustively. To address this need, we adapted a method used in population genetics, the parsimony test, to determine the relatedness of communities. Here we describe our implementation of the parsimony test, TreeClimber, in which we reanalyzed six previously published studies and compared the results of the analysis to those obtained using ∫-LIBSHUFF.

scholarly journals Microbial Population Changes during Bioremediation of an Experimental Oil Spill

1999 ◽  
Vol 65 (8) ◽  
pp. 3566-3574 ◽  
Author(s):  
Sarah J. MacNaughton ◽  
John R. Stephen ◽  
Albert D. Venosa ◽  
Gregory A. Davis ◽  
Yun-Juan Chang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Oil Spill ◽  
Phospholipid Fatty Acid ◽  
Community Structures ◽  
Gram Negative ◽  
Dgge Analysis ◽  
16S Rdna Pcr ◽  
Microbial Community Structures ◽  
Plfa Analysis

ABSTRACT Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria andFlexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.

scholarly journals Differences in the Concentration and Composition of Human Milk Components Are Related to Variation in Milk and Infant Fecal Microbiomes

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1056-1056
Author(s):  
Ryan Pace ◽  
Janet Williams ◽  
Kimberly Lackey ◽  
Mark McGuire ◽  
Michelle McGuire ◽  
...  
Keyword(s):  
Human Milk ◽  
Microbial Communities ◽  
Infant Health ◽  
Hypervariable Region ◽  
Fecal Microbiota ◽  
National Institutes Of Health ◽  
Funding Sources ◽  
Infant Feces ◽  
Microbe Interactions ◽  
Foundation Award

Abstract Objectives Profiles of human milk oligosaccharides (HMO) and milk/infant fecal microbiota vary globally. However, associations between and among HMO, other milk-borne factors (e.g., lactose, protein), and milk/infant fecal microbiomes have not been well-investigated. Here we tested the hypothesis that variations in milk lactose, protein, and HMO concentrations are associated with variations in the structure of milk and infant fecal microbial communities. Methods Milk/infant fecal samples from 357 maternal-infant dyads collected as part of the INSPIRE study from 11 geographically/culturally diverse sites located in eight countries (Ethiopia, The Gambia, Ghana, Kenya, Peru, Spain, Sweden, and USA) were analyzed. DNA was extracted and bacterial 16S rRNA V1V3 hypervariable region amplified/sequenced for microbiome analysis. HMO, lactose, and protein profiles were generated from HPLC and spectrophotometric assays. Results Milk and infant feces share many of the same abundant bacterial genera, while also containing unique bacterial communities. Community states type (CST) analyses indicate both sample types group into a relatively small number of discrete communities characterized by enrichment of specific taxa (e.g., Streptococcus, Bifidobacterium). Concentrations of milk lactose and protein varied by population/CST. Additionally, variation in the microbial community structure of milk and infant feces was associated with concentrations of total/individual HMO, lactose, and protein. Conclusions Similar to HMO concentrations, milk lactose and protein vary globally. Variations in milk and infant fecal microbial communities are associated with those of milk lactose, protein, and HMO concentrations. Given these results, as well as prior data on the influence of other environmental variables (e.g., pumped vs. direct breastfeeding), additional longitudinal studies are needed to better understand this complex network of maternal-infant-microbe interactions with respect to environmental factors and how differences impact postnatal maternal-infant health. Funding Sources National Science Foundation (award 1,344,288), National Institutes of Health (R01 HD092297), and USDA.

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