Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia

Background Secondary symbionts of insects include a range of bacteria and fungi that perform various functional roles on their hosts, such as fitness, tolerance to heat stress, susceptibility to insecticides, reproduction. These endosymbionts could have the potential to shape microbial communites and high potential to develop strategies for mosquito-borne disease control. Methodology/Principal findings The relative frequency and molecular phylogeny of Wolbachia, Microsporidia and Cardinium were determined of phlebotomine sand flies and mosquitoes in two regions from Colombia. Illumina Miseq using the 16S rRNA gene as a biomarker was conducted to examine the microbiota. Different percentages of natural infection by Wolbachia, Cardinium, and Microsporidia in phlebotomines and mosquitoes were detected. Phylogenetic analysis of Wolbachia shows putative new strains of Lutzomyia gomezi (wLgom), Brumptomyia hamata (wBrham), and a putative new group associated with Culex nigripalpus (Cnig) from the Andean region, located in Supergroup A and Supergroup B, respectively. The sequences of Microsporidia were obtained of Pi. pia and Cx. nigripalpus, which are located on phylogeny in the IV clade (terrestrial origin). The Cardinium of Tr. triramula and Ps. shannoni were located in group C next to Culicoides sequences while Cardinium of Mi. cayennensis formed two putative new subgroups of Cardinium in group A. In total were obtained 550 bacterial amplicon sequence variants (ASVs) and 189 taxa to the genus level. The microbiota profiles of Sand flies and mosquitoes showed mainly at the phylum level to Proteobacteria (67.6%), Firmicutes (17.9%) and Actinobacteria (7.4%). High percentages of relative abundance for Wolbachia (30%-83%) in Lu. gomezi, Ev. dubitans, Mi. micropyga, Br. hamata, and Cx. nigripalpus were found. ASVs assigned as Microsporidia were found in greater abundance in Pi. pia (23%) and Cx. nigripalpus (11%). An important finding is the detection of Rickettsia in Pi. pia (58,8%) and Bartonella sp. in Cx. nigripalpus. Conclusions/Significance We found that Wolbachia infection significantly decreased the alpha diversity and negatively impacts the number of taxa on sand flies and Culex nigripalpus. The Principal Coordinate Analysis (PCoA) is consistent, which showed statistically significant differences (PERMANOVA, F = 2.4744; R2 = 0.18363; p-value = 0.007) between the microbiota of sand flies and mosquitoes depending on its origin, host and possibly for the abundance of some endosymbionts (Wolbachia, Rickettsia).

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Responses of microbial community from tropical pristine coastal soil to crude oil contamination

10.7287/peerj.preprints.1254v1 ◽

2015 ◽

Author(s):

Daniel Morais ◽

Victor Pylro ◽

Ian M Clark ◽

Penny R Hirsch ◽

Marcos Tótola

Keyword(s):

Microbial Community ◽

Crude Oil ◽

Alpha Diversity ◽

Illumina Miseq ◽

Oil Reservoirs ◽

Rrna Gene ◽

Community Shift ◽

Campos Basin ◽

Trindade Island ◽

Bacteria And Fungi

Crude oil is still the dominant energy source in Brazil and that the consumption keeps rising since 2013, being responsible for 2.2% of the world’s energy consumption. The recent discovery of crude oil reservoirs at the Espirito Santo basin, Campos basin and Santos basin, can be considered as an excellent opportunity to supply the country’s economic and energetic demands. However, albeit the opportunity these crude oil reservoirs represent, offshore exploration offers risks to the microbiota and the whole sea life, as petroleum hydrocarbons are toxic, mutagenic, teratogenic and carcinogenic. Microbes are responsible for nutrient cycling and can degrade even very recalcitrant hydrocarbons. This work aimed to evaluate the microbial community shift (Archaea, Bacteria and Fungi) from Trindade Island coastal environment under petroleum contamination. Microcosms were assembled using Trindade Island coastal soil to create two treatments, control and contaminated (weathered crude oil at 30 g kg-1). Soils were incubated during 38 days with CO2 measurements every four hours. Total DNA was extracted, purified and submited for sequencing of 16s rRNA gene, for Bacteria and Archaea domains and Fungal ITS1 region using Illumina MiSeq platform. We compared alpha diversity, beta diversity and taxonomic shifts between controls and contaminated samples. Three days after contamination, emission rate peaked at more than 20x the control and the emissions remained higer during the whole incubation period. Microbial alpha diversity was reduced for contaminated-samples. Fungi community of contaminated samples was reduced to almost 40% of the observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum and reduction of the Archaea Candidatus nitrosphaere.

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Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

Current Developments in Nutrition ◽

10.1093/cdn/nzab027 ◽

2021 ◽

Author(s):

Maciej Chichlowski ◽

Nicholas Bokulich ◽

Cheryl L Harris ◽

Jennifer L Wampler ◽

Fei Li ◽

...

Keyword(s):

Infant Formula ◽

Beta Diversity ◽

Milk Fat ◽

Alpha Diversity ◽

Illumina Miseq ◽

Rrna Gene ◽

Term Infants ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration: https://clinicaltrials.gov/ct2/show/NCT02274883).

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The cultivation of Pyropia haitanensis has important impacts on the seawater microbial community

Journal of Applied Phycology ◽

10.1007/s10811-020-02068-6 ◽

2020 ◽

Vol 32 (4) ◽

pp. 2561-2573

Author(s):

Wenlei Wang ◽

Lei Wu ◽

Kai Xu ◽

Yan Xu ◽

Dehua Ji ◽

...

Keyword(s):

Microbial Community ◽

Growth And Development ◽

Alpha Diversity ◽

18S Rrna Gene ◽

Pyropia Haitanensis ◽

Rrna Gene ◽

Cultivation Period ◽

Rrna Gene Sequencing ◽

Bacteria And Fungi ◽

Surrounding Seawater

Abstract Microorganisms play important roles in the growth and development of macroalgae. Still, the biodiversity of the epiphytic microbial community associated with the economically important red alga Pyropia haitanensis during the cultivation period remains uncharacterized, especially the effects of P. haitanensis cultivation on the microbial community of surrounding seawater. Here, we isolated epiphytic microbes from P. haitanensis during the thallus stage during oceanic cultivation and the conchocelis stage during industrial cultivation. The dynamic diversity patterns, as determined by 16S and 18S rRNA gene sequencing of the bacterial and fungal communities, respectively, associated with P. haitanensis and seawater in the presence and absence of algal cultivation were investigated. A notable distinction was observed between the microbial communities of seawater with and without P. haitanensis cultivation. Additionally, the alpha-diversity of seawater with P. haitanensis cultivation was significantly greater than without P. haitanensis cultivation. Cyanobacteria were the dominant species in the latter, while Rhodobacteraceae was enriched in the former. Furthermore, there were significant differences in the microbial community of P. haitanensis at the thallus and conchocelis stages. Seawater properties had significant direct effects on the microbial diversity of P. haitanensis and cultivation seawater, but not on non-cultivation seawater. The enriched microbial presence might promote thallus morphogenesis and be beneficial for the growth and development of both the thallus and conchocelis stages. These findings expand our knowledge of the bacteria and fungi that are beneficial for Pyropia nursery seeding and cultivation, as well as the effects of P. haitanensis cultivation on the seawater microbial community.

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PSXIII-29 Farm of origin has a major influence on the colonic microbiome but alterations due to selection for feed efficiency are also evident

Journal of Animal Science ◽

10.1093/jas/skz258.932 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 475-475

Author(s):

Stafford Vigors ◽

Torres Sweeney

Keyword(s):

Feed Efficiency ◽

Hypervariable Region ◽

Alpha Diversity ◽

Illumina Miseq ◽

Nutrient Digestibility ◽

Major Influence ◽

Rrna Gene ◽

Diversity Analysis ◽

Selection For

Abstract While the intestinal microbiota is functionally important in nutrient digestibility and animal performance, the role of the microbiome in influencing feed efficiency is not well characterised. The objective of this experiment was to determine the relative influence of feed efficiency and farm of origin on the pig colonic microbiome. Animals were sourced from two geographically distinct locations in Ireland (farm A + B) and evaluated to identify pigs divergent in feed efficiency. The 8 most efficient (LRFI) & 8 least efficient (HRFI) pigs from farm A and 12 LRFI & 12 HRFI pigs from farm B were slaughtered. Colonic digesta was collected for sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed on the Illumina MiSeq. Alpha diversity differed between the farms in this study with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P < 0.05). In agreement with this observation, pigs grouped by farm of origin rather than RFI in the beta diversity analysis. However, despite variation between farms, interesting taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of two families BS11 (P < 0.05) and a tendency towards increased Bacteroidaceae (P < 0.10) relative to the HRFI group. At genus level, the LRFI pigs had a tendency towards increased Bacteroides and CF231 (P < 0.10). In conclusion, while farm of origin has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of feed efficiency status was evident.

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Regime Transition Shapes the Composition, Assembly Processes and Co-Occurrence Pattern of Bacterioplankton Community in a Large Eutrophic Freshwater Lake

10.21203/rs.3.rs-427021/v1 ◽

2021 ◽

Author(s):

Xinyi Cao ◽

Dayong Zhao ◽

Lisa Röttjers ◽

Karoline Faust ◽

Hongjie Zhang

Keyword(s):

Community Composition ◽

Regime Shift ◽

Alpha Diversity ◽

Illumina Miseq ◽

Nutrient Concentrations ◽

Rrna Gene ◽

Network Clustering ◽

Regime Transition ◽

Bacterioplankton Community ◽

Occurrence Pattern

Abstract At certain nutrient concentrations, shallow freshwater lakes are generally characterized by two contrasting ecological regimes with disparate patterns of biodiversity and biogeochemical cycles: a macrophyte-dominated regime (MDR) and a phytoplankton-dominated regime (PDR).To reveal ecological mechanisms that affect bacterioplankton along the regime shift, Illumina MiSeq sequencing of the 16S rRNA gene combined with a novel network clustering tool (Manta) were used to identify patterns of bacterioplankton community composition across the regime shift in Taihu Lake, China. Marked divergence in the composition and ecological assembly processes of bacterioplankton community were observed under the regime shift. The alpha diversity of bacterioplankton community was observed to consistently and continuously decrease with the regime shift from MDR to PDR, while the beta diversity presents the opposite. Moreover, as the regime shifted from MDR to PDR, the contribution of deterministic processes first decreased and then increased again closer to the PDR, most likely as a consequence of differences in nutrient concentration. The topological properties of bacterioplankton co-occurrence networks along the regime shift differed, and the co-occurrences among species changed in structure and were significantly shaped by the environmental variables along the regime transition from MDR to PDR. The divergent environmental state of the regimes with diverse nutritional status may be the most important factor that contributes to the dissimilarity of bacterioplankton community composition along the regime shift and could be represented by phosphorus concentrations as well as several indicator species.

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Responses of microbial community from tropical pristine coastal soil to crude oil contamination

PeerJ ◽

10.7717/peerj.1733 ◽

2016 ◽

Vol 4 ◽

pp. e1733 ◽

Cited By ~ 17

Author(s):

Daniel Morais ◽

Victor Pylro ◽

Ian M. Clark ◽

Penny R. Hirsch ◽

Marcos R. Tótola

Keyword(s):

Microbial Community ◽

Crude Oil ◽

Alpha Diversity ◽

Illumina Miseq ◽

Oceanic Islands ◽

Oil Contamination ◽

Target Sequencing ◽

Metabolic Functions ◽

Crude Oil Contamination ◽

Bacteria And Fungi

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg−1), in triplicate. Soils were incubated for 38 days, with CO2measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

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Comparative Analysis of Bacterial Communities in Lutzomyia ayacuchensis Populations with Different Vector Competence to Leishmania Parasites in Ecuador and Peru

Microorganisms ◽

10.3390/microorganisms9010068 ◽

2020 ◽

Vol 9 (1) ◽

pp. 68

Author(s):

Ahmed Tabbabi ◽

Shinya Watanabe ◽

Daiki Mizushima ◽

Abraham G. Caceres ◽

Eduardo A Gomez ◽

...

Keyword(s):

Comparative Analysis ◽

Vector Competence ◽

Illumina Miseq ◽

Sand Fly ◽

Leishmania Infection ◽

Rrna Gene ◽

Sand Flies ◽

Peruvian Andes ◽

Southern Peru ◽

Insect Gut

Differences in the gut microbial content of Lutzomyia (Lu.) ayacuchensis, a primary vector of Andean-type cutaneous leishmaniasis in Ecuador and Peru, may influence the susceptibility of these sand flies to infection by Leishmania. As a first step toward addressing this hypothesis, a comparative analysis of bacterial and fungal compositions from Lu. ayacuchensis populations with differential susceptibilities to Leishmania was performed. Bacterial 16S rRNA gene amplification and Illumina MiSeq sequencing approaches were used to characterize the bacterial composition in wild-caught populations from the Andean areas of Ecuador and southern Peru at which the sand fly species transmit Leishmania (Leishmania) mexicana and Leishmania (Viannia) peruviana, respectively, and a population from the northern Peruvian Andes at which the transmission of Leishmania by Lu. ayacuchensis has not been reported. In the present study, 59 genera were identified, 21 of which were widely identified and comprised more than 95% of all bacteria. Of the 21 dominant bacterial genera identified in the sand flies collected, 10 genera had never been detected in field sand flies. The Ecuador and southern Peru populations each comprised individuals of particular genera, while overlap was clearly observed between microbes isolated from different sites, such as the number of soil organisms. Similarly, Corynebacterium and Micrococcus were slightly more dominant bacterial genera in the southern Peru population, while Ochrobactrum was the most frequently isolated from other populations. On the other hand, fungi were only found in the southern Peru population and dominated by the Papiliotrema genus. These results suggest that variation in the insect gut microbiota may be elucidated by the ecological diversity of sand flies in Peru and Ecuador, which may influence susceptibility to Leishmania infection. The present study provides key insights for understanding the role of the microbiota during the course of L. (L.) mexicana and L. (V.) peruviana infections in this important vector.

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83 Lifelong dynamics of the swine gut microbiome: from birth to market

Journal of Animal Science ◽

10.1093/jas/skz122.087 ◽

2019 ◽

Vol 97 (Supplement_2) ◽

pp. 48-48

Author(s):

Xiaofan Wang ◽

Tsung Cheng Tsai ◽

Charles V Maxwell ◽

Jiangchao Zhao

Keyword(s):

Growth Performance ◽

Gut Microbiome ◽

Community Dynamics ◽

Alpha Diversity ◽

Illumina Miseq ◽

Shannon Index ◽

Growth Stages ◽

Rrna Gene ◽

16 S Rrna

Abstract Despite the recent advances in the swine gut microbiomes during different growth stages, a comprehensive longitudinal study of the lifelong dynamics of the swine gut microbiome is lacking. To fill this gap of knowledge, we selected seventeen piglets (PIC29*380) that were born on the same date from three sows. We collected a total of 274 rectal swabs during lactation (d 0, 11, 20), nursery (d 27, 33, 41, 50, 61), growing (d 76, 90, 104, 116), and finishing (d 130, 146, 159, and 174) stages. Samples were extracted using the Powersoil DNA isolation kit (Qiagen, Hilden, Germany) and sequenced with an Illumina Miseq sequencer targeting the V4 region of the 16 S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. In general, alpha diversity including community richness (e.g., number of observed features, Chao1) and diversity (e.g., Shannon Index) showed an overall trend of increasing from lactation to the finishing stage (P < 0.01). Gradual and significant changes in community structures were also observed along the four growth stages (ANOSIM, R = 0.66; P < 0.01). Non-parametric permutational multivariate analysis of variance shows that main factors driving the lifelong community dynamics included age and diet. Seventeen phylum members were discovered in the lifelong pig gut microbiome with Firmicutes and Bacteroidetes being the most abundant phyla. LEfSe analysis revealed 63 bacterial features that are stage specific. By using a regressing tree based Random Forest model we identified five bacterial features that are associated with swine growth performance including features 26 (Turicibacteraceae Turicibacter), 27 (Clostridium butyricum), 18 (Clostridiaceae), 19 (Clostridium perfringens) and 4 (Clostridiaceae). Characterization of the lifelong dynamics of 17 healthy pigs from birth to market provides a foundation for gut microbiome studies focusing on swine development, health and growth performance.

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Applications of Blocker Nucleic Acids and Non-Metazoan PCR Improves the Discovery of the Eukaryotic Microbiome in Ticks

Microorganisms ◽

10.3390/microorganisms9051051 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1051

Author(s):

Yurie Taya ◽

Gohta Kinoshita ◽

Wessam Mohamed Ahmed Mohamed ◽

Mohamed Abdallah Mohamed Moustafa ◽

Shohei Ogata ◽

...

Keyword(s):

Nucleic Acids ◽

Alpha Diversity ◽

Illumina Miseq ◽

18S Rrna Gene ◽

Rrna Gene ◽

Miseq Platform ◽

Pcr Method ◽

Almost All ◽

Tick Microbiome ◽

Generation Sequencing

Ticks serve as important vectors of a variety of pathogens. Recently, the viral and prokaryotic microbiomes in ticks have been explored using next-generation sequencing to understand the physiology of ticks and their interactions with pathogens. However, analyses of eukaryotic communities in ticks are limited, owing to the lack of suitable methods. In this study, we developed new methods to selectively amplify microeukaryote genes in tick-derived DNA by blocking the amplification of the 18S rRNA gene of ticks using artificial nucleic acids: peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). In addition, another PCR using non-metazoan primers, referred to as UNonMet-PCR, was performed for comparison. We performed each PCR using tick-derived DNA and sequenced the amplicons using the Illumina MiSeq platform. Almost all sequences obtained by conventional PCR were derived from ticks, whereas the proportion of microeukaryotic reads and alpha diversity increased upon using the newly developed method. Additionally, the PNA- or LNA-based methods were suitable for paneukaryotic analyses, whereas the UNonMet-PCR method was particularly sensitive to fungi. The newly described methods enable analyses of the eukaryotic microbiome in ticks. We expect the application of these methods to improve our understanding of the tick microbiome.

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Resident microbes of lactation rooms and daycares

PeerJ ◽

10.7717/peerj.8168 ◽

2019 ◽

Vol 7 ◽

pp. e8168

Author(s):

Diana H. Taft ◽

Samir Akre ◽

Nicolas Madrid ◽

Andre Knoesen ◽

David A. Mills ◽

...

Keyword(s):

Beta Diversity ◽

Alpha Diversity ◽

Illumina Miseq ◽

Shannon Index ◽

Rrna Gene ◽

Sample Collection ◽

Unifrac Distance ◽

Modern Development ◽

Temperature And Humidity ◽

The Impact

Dedicated lactation rooms are a modern development as mothers return to work while still providing breastmilk to their absent infants. This study describes the built environment microbiome of lactation rooms and daycares, and explores the influence of temperature and humidity on the microbiome of lactation rooms. Sterile swabs were used to collect samples from five different sites in lactation rooms at University of California, Davis and from five different sites in daycares located in Davis, California. DNA from the swabs was extracted and the V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Temperature and relative humidity data were collected on a subset of the lactation rooms. Sampled lactation rooms could be either dedicated lactation rooms or could also serve other functions (e.g., combined lactation room and restroom lounge). The majority of sequence reads were identified as belonging to family Moraxellaceae, with 73% of all reads included in analysis identified as an unknown species of Acinetobacter. Alpha diversity was analyzed using the Shannon index, while beta diversity was analyzed using unweighted and weighted UniFrac distance. The Jaccard distance was used to measure amount of change at sampling locations between time points for analysis of the impact of temperature and humidity on the microbiome. There were significant differences in the beta diversity of the microbiome of lactation rooms by room type. There were also significant differences in the beta diversity of the microbiome by sample collection location. There were no significant differences in either alpha or beta diversity associated with room temperature or humidity. Additional studies are needed to understand if the differences in lactation room type may result in differences in the breastmilk microbiome of milk collected in those rooms, and to what extent any such differences may influence the infant microbiome.

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