Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol

The first exposures to microbes occur during infancy and it is suggested that this initial colonization influences the adult microbiota composition. Despite the important role that the gut microbiome may have in health outcomes later in life, the factors that influence its development during infancy and early childhood have not been characterized fully. Guidelines about the introduction of solid foods and cessation of breastfeeding, which is thought to have a significant role in the transition to a more adult-like microbiota, are not based on microbiome research. There is even less understanding of approaches used to transition to solid food in the preterm population. The purpose of this study is to identify the impact of early life dietary events on gut microbiome community structures and function among infants born at term and pre-term. We plan to prospectively monitor the gut microbiome of infants during two critical timepoints in microbial development: the introduction of solid foods and cessation from breastmilk. A total of 35 participants from three primary observational birth cohorts (two full-term cohorts and one pre-term cohort) will be enrolled in this sub-study. Participants will be asked to collect stool samples and fill out a study diary before, during and after the introduction of solids and again during weaning from breastmilk. We will use frequent fecal sampling analyzed using 16S rRNA gene profiling, metagenomics, metabolomics, and targeted bacterial culturing to identify and characterize the microbial communities, as well as provide insight into the phenotypic characteristics and functional capabilities of the microbes present during these transitional periods of infancy. This study will provide a comprehensive approach to detailing the effects of dietary transition from breastmilk to a more adult-like solid food diet on the microbiome and in doing so will contribute to evidence-based infant nutrition guidance.

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Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts

Nutrients ◽

10.3390/nu13082639 ◽

2021 ◽

Vol 13 (8) ◽

pp. 2639

Author(s):

Chiara-Maria Homann ◽

Connor A. J. Rossel ◽

Sara Dizzell ◽

Liene Bervoets ◽

Julia Simioni ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiome ◽

Dietary Diversity ◽

Solid Food ◽

Microbial Composition ◽

Term Infants ◽

Negatively Associated ◽

Solid Foods ◽

Solid Food Introduction ◽

The Impact

The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food & Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray–Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced.

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Gut microbiota features of the geographically diverse Indian population

10.1101/478586 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sudarshan A. Shetty

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Indian Population ◽

Geographic Location ◽

Population Level ◽

Gene Profiling ◽

Rrna Gene ◽

Base Line ◽

Microbiome Composition ◽

And Function

AbstractPopulation-level microbial profiling allows for identifying the overarching features of the microbiome. Knowledge of population specific base-line gut microbiome features is important due to the widely reported impact of geography, lifestyle and dietary patterns on the microbiome composition, structure and function. Here, the gut microbiota of more than 1000 subjects across the length and breadth of India is presented. The publicly available 16S rRNA gene profiling data of faecal microbiota from the Landscape Of Gut Microbiome - Pan-India Exploration (LogMPIE) study representing 14 major cities, covering populations from northern, southern, eastern and western part of India analyzed. Majority of the dominant OTUs belonged to the Firmicutes, Bacteroidetes and Proteobacteria phyla. The rarer fraction was comprised of OTUs mainly from the phyla Verrucomicrobia and Spirochaetes. The median core size was estimated to consist of 12 OTUs (>80% prevalence) dominated by representing genera Prevotella, Faecalibacterium, Bacteroides, Roseburia, Megasphaera, Eubacterium and Gemmiger. Geographic location explained majority of the variation in the gut microbiota community structure. The observations of the present study support the previous reports of Prevotella dominance in the Indian population. The Prevotella/Bacteroides ratio was high for the overall population irrespective of geographic location and did not correlate with BMI or age of the participants. Despite a rapid transition towards a western lifestyle, high prevalence of Treponema in the Indian gut microbiota suggests that the urban population still harbors signatures of the traditional gut microbiome. The results presented here improve the knowledge of baseline microbiota in the Indian population across the length and breadth of the country. This study provides a base for future studies which need to incorporate numerous other confounding factors and their impact on the observed characteristics of the Indian gut microbiome.

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132 Early Establishment of the Human Gut Microbiome—a Tale of Moms, Their Diets, and Babes Guts

Journal of Animal Science ◽

10.1093/jas/skab235.123 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 68-68

Author(s):

Kjersti M Aagaard

Keyword(s):

Gut Microbiome ◽

Maternal Obesity ◽

Maternal Diet ◽

Dietary Exposure ◽

Metabolic Phenotype ◽

Strong Impact ◽

High Fat ◽

Lower Genital Tract ◽

And Function ◽

The Impact

Abstract Human microbial communities are characterized by their metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. We are only beginning to characterize the complex set of interactions which alters both community membership and function in early development. With respect to the potential source of microbiota at birth, it has been generally assumed that the majority of seeding microbes originate from the maternal lower genital tract, with microbiota ascending into the otherwise sterile intrauterine. However, we and subsequently others have recently demonstrated that (1) the vaginal and gut microbiome communities are distinctly structured in pregnancy, and (2) the intrauterine environment and the fetus is in fact not sterile, but rather harbors a low-abundance microbiome which varies by several measured exposures, and (3) the maternal diet during both gestation and lactation, and notably a high fat diet, has a particularly strong impact on the developing and early in life microbial community structure. We have taken two dynamic approaches to answering these questions in our studies. First, we use large and robust longitudinal cohorts of maternal-infant dyads collected across gestation and into infancy to gain deeper insight into both source and sink of the early developmental microbiome and its role on determining length of gestation. Second, we utilize our well established primate models of maternal high fat dietary exposure, both in the absence and presence of maternal obesity, to determine the impact of maternal diet on both the microbiome and the resultant offspring metabolic phenotype.

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Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut

mSystems ◽

10.1128/msystems.00612-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 5

Author(s):

Anders Janzon ◽

Julia K. Goodrich ◽

Omry Koren ◽

Jillian L. Waters ◽

Ruth E. Ley

Keyword(s):

Gut Microbiome ◽

Immunoglobulin A ◽

Gene Profiling ◽

Rrna Gene ◽

Bacterial Cells ◽

Future Health ◽

Operational Taxonomic Units ◽

Single Location ◽

Infant Gut Microbiome ◽

Antibody Coating

ABSTRACT Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during infancy are important for future health. IgM and IgG are also present in the gut; however, their interactions with the microbiome in the developing infant remain to be characterized. Using stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries, we characterized patterns of microbiome development in relation to fecal levels of IgA, IgG, and IgM. For 8 infants from a single location, we used fluorescence-activated cell sorting of microbial cells from stool by Ig-coating status over 18 months. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors. All antibodies decreased in concentration with age but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with relative abundances of operational taxonomic units (OTUs) belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus. The diversity of Ig-coated microbiota was influenced by breastfeeding and age. IgA and IgM coated the same microbiota, which reflected the overall diversity of the microbiome, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M. IgA/M displayed similar dynamics, generally coating the microbiome proportionally, and were influenced by breastfeeding status. IgG only coated a small fraction of the commensal microbiota and differed from the proportion targeted by IgA and IgM. IMPORTANCE Antibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby’s own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of bacteria in the infant gut as the infant develops from birth to 18 months old and how patterns of antibody coating of bacteria change with age. In this study of healthy infant samples over time, we found that IgA and IgM coat the same bacteria, which are generally representative of the diversity present, with a few exceptions that were more or less antibody coated than expected. IgG coated a separate suite of bacteria. These results provide a better understanding of how these antibodies interact with the developing infant gut microbiome.

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Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions

Applied and Environmental Microbiology ◽

10.1128/aem.02189-20 ◽

2021 ◽

Author(s):

A. Shore ◽

R. D. Day ◽

J. A. Stewart ◽

C.A. Burge

Keyword(s):

Ocean Acidification ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Ph Gradient ◽

Rrna Gene ◽

Seawater Ph ◽

Coral Health ◽

And Function ◽

The Impact

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean. IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

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Effect of Salinity on the Gut Microbiome of Pike Fry (Esox lucius)

Applied Sciences ◽

10.3390/app10072506 ◽

2020 ◽

Vol 10 (7) ◽

pp. 2506

Author(s):

Tomasz Dulski ◽

Roman Kujawa ◽

Martyna Godzieba ◽

Slawomir Ciesielski

Keyword(s):

Gut Microbiome ◽

High Salinity ◽

Fish Farming ◽

Amplicon Sequencing ◽

Good Alternative ◽

Control Group ◽

Rrna Gene ◽

Microbiological Analysis ◽

Early Life Stages ◽

The Impact

The increasing popularity of pike in angling and fish farming has created a need to increase pike production. However, intensive pike farming is subject to limitations due to diseases and pathogens. Sodium chloride (NaCl) could be a good alternative to chemotherapeutics, especially for protecting the fish against pathogens and parasites at early life stages. However, the impact of high salinity on the symbiotic bacteria inhabiting freshwater fish is still unclear. Therefore, our objective was to analyze the gut microbiome to find possible changes caused by salinity. In this study, the influence of 3‰ and 7‰ salinity on pike fry was investigated. High-throughput 16S rRNA gene amplicon sequencing was used to profile the gut microbiome of the fish. It was found that salinity had a statistically significant influence on pike fry mortality. Mortality was highest in the 7‰ salinity group and lowest in the 3‰ group. Microbiological analysis indicated that Proteobacteria and Actinobacteria predominated in the pike gut microbiome in all examined groups, followed by lower percentages of Bacteroidetes and Firmicutes. There were no statistically significant differences in the percent abundance of bacterial taxa between the control group and groups with a higher salinity. Our results suggest that salinity influences the gut microbiome structure in pike fry, and that 3‰ salinity may be a good solution for culturing pike at this stage in their development.

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The milk-based diet of infancy and the gut microbiome

Gastroenterology Report ◽

10.1093/gastro/goz031 ◽

2019 ◽

Vol 7 (4) ◽

pp. 246-249 ◽

Cited By ~ 1

Author(s):

Hu Hao ◽

Lixin Zhu ◽

Howard S Faden

Keyword(s):

Human Milk ◽

Gut Microbiome ◽

Well Being ◽

Solid Food ◽

Poor Health ◽

Commensal Bacterium ◽

Essential Nutrients ◽

The Impact ◽

Health And Well Being ◽

Food Complex

Abstract The composition and the diversity of the gut microbiome play a major role in the health and well-being of humans beginning at birth. The impact of the diet on the structure and the function of the gut microbiome is evident by the changes in the gut microbiome concurrent with the transition from human milk to solid food. Complex oligosaccharides contained in milk are essential nutrients for commensal microbes in the infant gut. The most important commensal bacterium in the infant gut, bifidobacterium, requires α1, 2 fucosylated oligosaccharides for growth. Because not all humans are able to secrete α1, 2 fucosylated oligosaccharides into milk, the gut microbiome of infants and bifidobacteria, in particular, vary considerably between ‘secretors’ and ‘non-secretors’. A paucity of α1, 2 fucosylated oligosaccharides and bifidobacteria in the gut of infants may be associated with poor health.

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Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome

mBio ◽

10.1128/mbio.01343-17 ◽

2017 ◽

Vol 8 (5) ◽

Cited By ~ 89

Author(s):

Tanja V. Maier ◽

Marianna Lucio ◽

Lang Ho Lee ◽

Nathan C. VerBerkmoes ◽

Colin J. Brislawn ◽

...

Keyword(s):

Lipid Metabolism ◽

Gut Microbiome ◽

Resistant Starch ◽

Metabolic Pathways ◽

Bacterial Species ◽

Human Microbiome ◽

Rrna Gene ◽

Gut Microbes ◽

Mechanistic Understanding ◽

The Impact

ABSTRACT Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of “omics” approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics. This multiomics approach captured changes in the abundance of specific bacterial species, proteins, and metabolites after a diet high in resistant starch (HRS), providing key insights into the influence of dietary interventions on the gut microbiome. The combined data showed that a high-RS diet caused an increase in the ratio of Firmicutes to Bacteroidetes , including increases in relative abundances of some specific members of the Firmicutes and concurrent increases in enzymatic pathways and metabolites involved in lipid metabolism in the gut. IMPORTANCE This work was undertaken to obtain a mechanistic understanding of the complex interplay between diet and the microorganisms residing in the intestine. Although it is known that gut microbes play a key role in digestion of the food that we consume, the specific contributions of different microorganisms are not well understood. In addition, the metabolic pathways and resultant products of metabolism during digestion are highly complex. To address these knowledge gaps, we used a combination of molecular approaches to determine the identities of the microorganisms in the gut during digestion of dietary starch as well as the metabolic pathways that they carry out. Together, these data provide a more complete picture of the function of the gut microbiome in digestion, including links between an RS diet and lipid metabolism and novel linkages between specific gut microbes and their metabolites and proteins produced in the gut.

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Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants

Clinical Infectious Diseases ◽

10.1093/cid/ciy882 ◽

2018 ◽

Vol 69 (2) ◽

pp. 268-277 ◽

Cited By ~ 21

Author(s):

S Graspeuntner ◽

S Waschina ◽

S Künzel ◽

N Twisselmann ◽

T K Rausch ◽

...

Keyword(s):

Preterm Infants ◽

Gut Microbiome ◽

Late Onset ◽

Anaerobic Bacteria ◽

Gene Profiling ◽

Rrna Gene ◽

Coagulase Negative Staphylococci ◽

Fermentation Products ◽

Gut Dysbiosis ◽

Late Onset Sepsis

Abstract Background Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome, including metabolic profiles, in preterm infants <34 weeks of gestation preceding LOS. Methods In a single-center cohort, fecal samples from preterm infants were prospectively collected during the period of highest vulnerability for LOS (days 7, 14, and 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics. Results We studied stool samples from 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). In most cases, the bacteria isolated in diagnostic blood culture corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci) and a lack of anaerobic bacteria. In silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease. Conclusions Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.

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Dynamic gut microbiome changes to low-iron challenge

Applied and Environmental Microbiology ◽

10.1128/aem.02307-20 ◽

2020 ◽

Author(s):

Genevieve L. Coe ◽

Nicholas V. Pinkham ◽

Arianna I. Celis ◽

Christina Johnson ◽

Jennifer L. DuBois ◽

...

Keyword(s):

Mouse Model ◽

Gut Microbiome ◽

Iron Homeostasis ◽

Human Microbiome ◽

Taxonomic Structure ◽

Dietary Iron ◽

Iron Cycling ◽

Highly Sensitive ◽

And Function ◽

The Impact

Iron is an essential micronutrient for life. In mammals, dietary iron is primarily absorbed in the small intestine. Currently, the impacts of dietary iron on the taxonomic structure and function of the gut microbiome and reciprocal effects on the animal host are not well understood. Here, we establish a mouse model of low-iron challenge in which intestinal biomarkers and reduced fecal iron reveal iron stress while serum iron and mouse behavioral markers indicate maintenance of iron homeostasis. We show that the diversity of the gut microbiome in conventional C57BL/6 mice changes dramatically during two-weeks on a low-iron diet. We also show the effects of a low-iron diet on microbiome diversity are long-lasting and not easily recovered when iron is returned to the diet. Finally, after optimizing taxon association methods, we show that some bacteria are unable to fully recover after the low-iron challenge and appear to be extirpated from the gut entirely. In particular, OTUs from the Prevotellaceae and Porphyromonadaceae families and Bacteroidales order are highly sensitive to low-iron conditions, while other seemingly insensitive OTUs recover. These results provide new insights into the iron requirements of gut microbiome members and add to the growing understanding of mammalian iron cycling. IMPORTANCE All cells need iron. Both too much iron and too little lead to diseases and unwanted outcomes. Although the impact of dietary iron on human cells and tissues has been well studied, there is currently a lack of understanding about how different levels of iron influence the abundant and diverse members of the human microbiome. This study develops a well-characterized mouse model for studying low-iron levels and identifies key groups of bacteria that are most affected. We found that the microbiome undergoes large changes when iron is removed from the diet but that many individual bacteria are able to rebound when iron levels are changed by to normal. That said, a select few members, referred to as “iron-sensitive” bacteria seem to be lost. This study begins to identify individual members of the mammalian microbiome most affected by changes in dietary iron levels.

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