Bacterial Co-Occurrence Patterns Between Human Milk and Microbial Sites of Breastfeeding Dyads

Abstract Objectives The human milk (HM) microbiota is predicted to originate from the maternal gastrointestinal tract, saliva and breast skin, and infant saliva. Though compositionally distinct, these habitats are strongly associated during breastfeeding. Vertical microbial transmission from mother to infant has been documented, but complex microbial interactions between sites are less clear. Herein, ecological networks between HM bacteria and other microbial sites of breastfeeding dyads were assessed to investigate the origin of the HM microbiota and how it may shape the infant gut microbiota. Methods DNA was extracted from maternal and infant saliva, HM, breast skin, and maternal and infant stool samples collected at 6 weeks postpartum from 33 mother-infant pairs. The V3-V4 region of the 16S rRNA gene was sequenced and taxonomy was assigned using QIIME 2. Co-occurrence patterns among genus-level abundance data were analyzed in CoNet (Cytoscape 3.0). Results Twenty-one significant co-presence relationships were identified between HM and other microbial communities. Associations spanned from six nodes in HM including Corynebacterium, Cutibacterium, Gemella, Rothia, Veillonella, and Actinomyces. Co-presence between Cutibacterium, Veillonella, Actinomyces, and Corynebacterium on skin and HM were identified, supporting breast skin as a principal contributor to the HM microbiota. Interestingly, Bifidobacterium in infant saliva was associated with Gemella and Rothia in HM. The greatest number of relationships existed between HM and infant stool. HM Gemella, Actinomyces, and Corynebacterium were associated with Bacteroides in infant stool; HM Actinomyces was also associated with infant fecal Escherichia-Shigella and Eggerthella. Additional relationships were identified between HM and maternal saliva and fecal microbiota. Conclusions Several unique ecological relationships exist between HM and microbial sites of breastfeeding dyads. Whether these relationships are indicative of proximity, mutualism, or are biomarkers of other host-microbe interactions remains to be determined. These data will be useful to uncover mechanisms driving microbial community organization and potential targets for microbial modulation in this population. Funding Sources National Dairy Council, NIH, The Gerber Foundation, The Doris Kelley Christopher Foundation.

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

Current Developments in Nutrition ◽

10.1093/cdn/nzaa054_128 ◽

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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Spatial metabolomics of in situ, host-microbe interactions

10.1101/555045 ◽

2019 ◽

Cited By ~ 2

Author(s):

Benedikt K Geier ◽

Emilia Sogin ◽

Dolma Michellod ◽

Moritz Janda ◽

Mario Kompauer ◽

...

Keyword(s):

Microbial Interactions ◽

Host Cells ◽

Metabolic Phenotype ◽

Community Members ◽

Metabolic Phenotypes ◽

Culture Independent ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Atmospheric Pressure Mass Spectrometry

Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric pressure mass spectrometry imaging (AP-MALDI-MSI) to image host-microbe symbioses and their metabolic interactions. metaFISH aligns and integrates metabolite and fluorescent images at the micrometer-scale for a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts, a variation in metabolic phenotypes in one symbiont type, and novel symbiosis metabolites. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ - a powerful tool for microbiologists across fields.

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Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere

Applied and Environmental Microbiology ◽

10.1128/aem.01321-10 ◽

2010 ◽

Vol 76 (24) ◽

pp. 8117-8125 ◽

Cited By ~ 114

Author(s):

Paul J. Hunter ◽

Paul Hand ◽

David Pink ◽

John M. Whipps ◽

Gary D. Bending

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Population Diversity ◽

Microbial Interactions ◽

Soluble Carbohydrates ◽

Rrna Gene ◽

Species Variation ◽

Clone Libraries ◽

Microbe Interactions

ABSTRACT Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

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Microbial interactions in the mosquito gut determine Serratia colonization and blood-feeding propensity

The ISME Journal ◽

10.1038/s41396-020-00763-3 ◽

2020 ◽

Vol 15 (1) ◽

pp. 93-108

Author(s):

Elena V. Kozlova ◽

Shivanand Hegde ◽

Christopher M. Roundy ◽

George Golovko ◽

Miguel A. Saldaña ◽

...

Keyword(s):

Vector Competence ◽

Inverse Correlation ◽

Blood Feeding ◽

Microbial Interactions ◽

Host Behavior ◽

Microbiome Analysis ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Native Host ◽

Mosquito Behavior

AbstractHow microbe–microbe interactions dictate microbial complexity in the mosquito gut is unclear. Previously we found that, Serratia, a gut symbiont that alters vector competence and is being considered for vector control, poorly colonized Aedes aegypti yet was abundant in Culex quinquefasciatus reared under identical conditions. To investigate the incompatibility between Serratia and Ae. aegypti, we characterized two distinct strains of Serratia marcescens from Cx. quinquefasciatus and examined their ability to infect Ae. aegypti. Both Serratia strains poorly infected Ae. aegypti, but when microbiome homeostasis was disrupted, the prevalence and titers of Serratia were similar to the infection in its native host. Examination of multiple genetically diverse Ae. aegypti lines found microbial interference to S. marcescens was commonplace, however, one line of Ae. aegypti was susceptible to infection. Microbiome analysis of resistant and susceptible lines indicated an inverse correlation between Enterobacteriaceae bacteria and Serratia, and experimental co-infections in a gnotobiotic system recapitulated the interference phenotype. Furthermore, we observed an effect on host behavior; Serratia exposure to Ae. aegypti disrupted their feeding behavior, and this phenotype was also reliant on interactions with their native microbiota. Our work highlights the complexity of host–microbe interactions and provides evidence that microbial interactions influence mosquito behavior.

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Probiotics in human milk and probiotic supplementation in infant nutrition: a workshop report

British Journal Of Nutrition ◽

10.1017/s0007114514001949 ◽

2014 ◽

Vol 112 (7) ◽

pp. 1119-1128 ◽

Cited By ~ 31

Author(s):

Henrike Bergmann ◽

Juan Miguel Rodríguez ◽

Seppo Salminen ◽

Hania Szajewska

Keyword(s):

Human Milk ◽

Infant Health ◽

Infant Nutrition ◽

Mode Of Delivery ◽

Bacterial Strains ◽

Probiotic Supplementation ◽

Maternal Environment ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Transfer To Milk

Probiotics in human milk are a very recent field of research, as the existence of the human milk microbiome was discovered only about a decade ago. Current research is focusing on bacterial diversity and the influence of the maternal environment as well as the mode of delivery on human milk microbiota, the pathways of bacterial transfer to milk ducts, possible benefits of specific bacterial strains for the treatment of mastitis in mothers, and disease prevention in children. Recent advances in the assessment of early host–microbe interactions suggest that early colonisation may have an impact on later health. This review article summarises a scientific workshop on probiotics in human milk and their implications for infant health as well as future perspectives for infant feeding.

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Microbial interactions in the mosquito gut determine Serratia colonization and blood feeding propensity.

10.1101/2020.04.14.039701 ◽

2020 ◽

Author(s):

Elena V Kozlova ◽

Shivanand Hegde ◽

Christopher M Roundy ◽

George Golovko ◽

Miguel A Saldana ◽

...

Keyword(s):

Vector Competence ◽

Inverse Correlation ◽

Blood Feeding ◽

Microbial Interactions ◽

Microbiome Analysis ◽

Mosquito Behaviour ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Host Behaviour ◽

Native Host

How microbe-microbe interactions dictate microbial complexity in the mosquito gut is unclear. Previously we found that Serratia, a gut symbiont that alters vector competence and is being considered for vector control, poorly colonized Aedes aegypti yet was abundant in Culex quinquefasciatus reared under identical conditions. To investigate the incompatibility between Serratia and Ae. aegypti, we characterized two distinct strains of Serratia marcescens from Cx. quinquefasciatus and examined their ability to infect Ae. aegypti. Both Serratia strains poorly infected Ae. aegypti, but when microbiome homeostasis was disrupted, the prevalence and titers of Serratia were similar to the infection in its native host. Examination of multiple genetically diverse Ae. aegypti lines found microbial interference to S. marcescens was commonplace, however one line of Ae. aegypti was susceptible to infection. Microbiome analysis of resistant and susceptible lines indicated an inverse correlation between Enterobacteriaceae bacteria and Serratia, and experimental co-infections in a gnotobiotic system recapitulated the interference phenotype. Furthermore, we observed an effect on host behaviour; Serratia exposure to Ae. aegypti disrupted their feeding behaviour, and this phenotype was also reliant on interactions with their native microbiota. Our work highlights the complexity of host-microbe interactions and provides evidence that microbial interactions influence mosquito behaviour.

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Saccharomyces cerevisiae found in the crop of a Neotropical Drosophila species fly collected in a natural forest remnant – comments on Hoang, Kopp & Chandler (2015)

10.7287/peerj.preprints.2090v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Marcos R. D. Batista ◽

Ana R. O. Santos ◽

Rafael D. Chaves ◽

Carlos A. Rosa ◽

Louis B. Klaczko

Keyword(s):

Saccharomyces Cerevisiae ◽

Invasive Species ◽

Yeast Species ◽

Natural Forest ◽

Rrna Gene ◽

Forest Fragment ◽

Forest Environment ◽

Forest Remnant ◽

Microbe Interactions ◽

Host Microbe Interactions

Abstract Background. Hoang, Kopp & Chandler (2015) questioned the use of commercial Saccharomyces cerevisiae as a model for investigating Drosophila – yeast association, since this approach “may not be fully representative of host-microbe interactions as they operate in nature”. They also claimed: “S. cerevisiae is rarely found with natural populations of D. melanogaster or other Drosophila species”. Indeed, previous choice experiments found that Sophophora subgenus flies (including invasive species D. melanogaster) are more attracted to banana baits inoculated with apiculate yeasts such as Hanseniaspora uvarum over S. cerevisiae inoculated baits. Yet, the forest interior dwelling species (FIDS) D. tripunctata group flies choose preferentially S. cerevisiae inoculated baits over H. uvarum in a natural forest environment. Aim and Methods. Our objective was to carry out a pilot experiment to examine yeast species associated with Drosophila in a natural Atlantic Rainforest fragment, especially examining, the yeast found with FIDS of the D. tripunctata group. We sampled Drosophila in a natural population from a Neotropical forest fragment. Males were dissected for isolating yeast colonies from their crops and to use their genitalia for species identification. Yeast species were identified by sequencing the D1/D2 domains of the 26S rRNA gene. Results and Conclusion. We isolated five yeast species from crops of Drosophila species of tripunctata group, including one strain of S. cerevisiae (from D. paraguayensis), confirming a previous record of S. cerevisiae isolates from a few tripunctata group species. Thus, their contention that “the results from D. melanogaster–S. cerevisiae laboratory experiments may not be fully representative of host–microbe interactions in nature” is probably right, but because D. melanogaster is an invasive species that is preferentially attracted in forests to apiculate yeasts, yet S. cerevisiae may be associated with FIDS Drosophila such as D. paraguayensis.

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Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome

PeerJ ◽

10.7717/peerj.5166 ◽

2018 ◽

Vol 6 ◽

pp. e5166 ◽

Cited By ~ 21

Author(s):

Jun Miyoshi ◽

Vanessa Leone ◽

Kentaro Nobutani ◽

Mark W. Musch ◽

Kristina Martinez-Guryn ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Standard Operating Procedure ◽

Individual Variability ◽

Rrna Gene ◽

Murine Models ◽

Single Room ◽

Specific Pathogen ◽

Microbe Interactions ◽

Host Microbe Interactions

Murine models are widely used to explore host-microbe interactions because of the challenges and limitations inherent to human studies. However, microbiome studies in murine models are not without their nuances. Inter-individual variations in gut microbiota are frequent even in animals housed within the same room. We therefore sought to find an efficient and effective standard operating procedure (SOP) to minimize these effects to improve consistency and reproducibility in murine microbiota studies. Mice were housed in a single room under specific-pathogen free conditions. Soiled cage bedding was routinely mixed weekly and distributed among all cages from weaning (three weeks old) until the onset of the study. Females and males were separated by sex and group-housed (up to five mice/cage) at weaning. 16S rRNA gene analyses of fecal samples showed that this protocol significantly reduced pre-study variability of gut microbiota amongst animals compared to other conventional measures used to normalize microbiota when large experimental cohorts have been required. A significant and consistent effect size was observed in gut microbiota when mice were switched from regular chow to purified diet in both sexes. However, sex and aging appeared to be independent drivers of gut microbial assemblage and should be taken into account in studies of this nature. In summary, we report a practical and effective pre-study SOP for normalizing the gut microbiome of murine cohorts that minimizes inter-individual variability and resolves co-housing problems inherent to male mice. This SOP may increase quality, rigor, and reproducibility of data acquisition and analysis.

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Disentangling Archaeal and Bacterial Biogeography and Co-occurrence Networks in Subtropical Mangrove Sediments Under Spartina Alterniflora Invasion

10.21203/rs.3.rs-113333/v1 ◽

2020 ◽

Author(s):

Weidong Chen ◽

Donghui Wen

Keyword(s):

Spartina Alterniflora ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Mangrove Ecosystem ◽

Microbial Interactions ◽

Rrna Gene ◽

Relative Role ◽

Ecological Processes ◽

Rare Taxa ◽

Occurrence Patterns

Abstract Background: Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora invasion in China. Large knowledge gaps remain with regard to archaeal and bacterial communities assembly processes and microbial interactions under S. alterniflora invasion. Here, using 16S rRNA gene amplicon sequencing, we investigated the assembly processes and co-occurrence relationships of the archaeal and bacterial communities under S. alterniflora invasion along the coastlines of Fujian province, southeast China.Results: We found that the overall archaeal and bacterial communities were driven predominantly by stochastic processes, and the relative role of stochasticity was stronger for bacteria than archaea. Co-occurrence network analysis showed that the network structure of bacteria was more complex than that of the archaea. Putative keystone taxa often had low relative abundances (conditionally rare taxa), suggesting conditionally rare taxa or low abundances taxa may significantly contribute to network stability. Moreover, we found that S. alterniflora invasion changed the microbial communities assembly and co-occurrence patterns, indicating that S. alterniflora affected the composition and stability of the microbial community.Conclusions: This study provides the first comparison in the biogeography and co-occurrence patterns of both archaea and bacteria in mangrove ecosystem. And this is the first exploration about the effect of S. alterniflora invasion on archaeal and bacterial ecological processes and co-occurrence patterns. Our study considers that the control of S. alterniflora invasion is important for mangrove ecosystem function and service.

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Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

Applied and Environmental Microbiology ◽

10.1128/aem.00956-12 ◽

2012 ◽

Vol 78 (17) ◽

pp. 6153-6160 ◽

Cited By ~ 56

Author(s):

Elizabeth A. Maga ◽

Prerak T. Desai ◽

Bart C. Weimer ◽

Nguyet Dao ◽

Dietmar Kültz ◽

...

Keyword(s):

Human Milk ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Fecal Microbiota ◽

Rrna Gene ◽

Gut Health ◽

Content Type ◽

Microbiome Composition ◽

The Impact ◽

Over Time

ABSTRACTHuman milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels ofFirmicutes(Clostridia) declined whereas those ofBacteroidetesincreased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P< 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (BifidobacteriaceaeandLactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae,Streptococcaceae,Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community.

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