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Microbiome

Microbiome

The collective microorganisms and their genomic elements and interactions in a particular environment.

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Edits on 11 Apr 2019
Carla Faraguna
Carla Faraguna approved a suggestion from Golden's AI on 11 Apr 2019 11:13 pm
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Several connections between skin and gut microbiota dysbiosis have been found. AD has been associated with changes in gut microbiota, with lower levels of Bifidobacterium in the gut than controls. Some studies have shown alterations in gut microbiota composition preceding AD, such as colonization with C. difficile and low Bacteriodetes diversity. In children with AD, whole-metagenome analysis showed depletion of mucin-degrading bacteria such as Akkermansia muciniphila, RuminococcusRuminococcus gnavus and Lachnospiraceae, bacteria that can influence the immune development. 

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 11 Apr 2019 7:37 pm
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The Canadian Healthy Infant Longitudinal Development (CHILD) study found a lower abundance of bacteria of the genera Lachnospira, VeillonellaVeillonella, Faecalibacterium and Rothia in the gut was associated with asthma later in life and linked mechanistically to reduced faecal short-chain fatty acids (SCFAs). High levels of SCFAs in early life have been shown to be protective against sensitization and asthma later in life. In as US study on a birth cohort, changes in relative abundance of certain microbes in the gut of neonates increased risk of multisensitized atopy and asthma. The children at increased risk had increased pro-inflammatory metabolites including those that induce IL-4 production in CD4+ T cells and decrease abundance of regulatory T cells (Tregs).

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 11 Apr 2019 7:28 pm
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Several connections between skin and gut microbiota dysbiosis have been found. AD has been associated with changes in gut microbiota, with lower levels of Bifidobacterium in the gut than controls. Some studies have shown alterations in gut microbiota composition preceding AD, such as colonization with C. difficile and low Bacteriodetes diversity. In children with AD, whole-metagenome analysis showed depletion of mucin-degrading bacteria such as Akkermansia muciniphilaAkkermansia muciniphila, Ruminococcus gnavus and Lachnospiraceae, bacteria that can influence the immune development. 

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 11 Apr 2019 7:08 pm
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The field of microbiomics, in which all microorganisms in a community or microbiota are analysed together, uses high-throughput DNA sequencing and RNA sequencing technologies and bioinformatics. Sample DNA is amplified and sequenced and compared to microbial genomic databases to find out the identities and diversity of microbes. Mass spectrometryMass spectrometry and nuclear magnetic resonance spectroscopy are used to analyze metabolic interactions between the microbiome and host.

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 11 Apr 2019 6:51 pm
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Most human studies on neonates suggest that contact with maternal and environmental microbes establishes early colonizers of the infant intestine. Vaginally delivered babies have microbial communities in their intestine dominated by LactobacillusLactobacillus spp. And Bifidobacterium spp., which are similarly found in the vaginal canal of their mothers. Babies delivered by cesarean section are colonized predominantly by skin microbes with Staphylococcus being the predominant genus. The neonatal gut provides a selective environment, allowing some organisms to colonize and inhibiting others.

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 11 Apr 2019 6:50 pm
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Atopic dermatitisAtopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, Acinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

Meredith Hanel
Meredith Hanel approved a suggestion from Golden's AI on 11 Apr 2019 6:26 pm
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Article (+13/-13 characters)

Article

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, AcinetobacterAcinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

Edits on 10 Apr 2019
Meredith Hanel
Meredith Hanel edited on 10 Apr 2019 3:01 am
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Article (+892 characters)

Article

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, Acinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

...

Several connections between skin and gut microbiota dysbiosis have been found. AD has been associated with changes in gut microbiota, with lower levels of Bifidobacterium in the gut than controls. Some studies have shown alterations in gut microbiota composition preceding AD, such as colonization with C. difficile and low Bacteriodetes diversity. In children with AD, whole-metagenome analysis showed depletion of mucin-degrading bacteria such as Akkermansia muciniphila, Ruminococcus gnavus and Lachnospiraceae, bacteria that can influence the immune development. 

...



Receptors on the cell surface of immune cells, such as toll-like receptors (TLRs) recognize pathogen-associated molecular patterns (PAMPs) from microorganisms from components such as lipopolysaccharides (LPS), peptidoglycans, lipoteichoic acid, flagellin and muramyldipeptide. Constituents of gram-negative bacteria such as LPS have been found to help trigger low-grade inflammation and insulin resistance through interaction between receptors in the innate immune system and gut microbes. Increased circulating LPS is a condition called metabolic endotoxaemia that has been found in genetic models of diet-induced obesity and diabetes as well as in humans. 



The gut barrier, that separates the intestinal lumen from the inside of the body, is controlled by communication between gut microbes and the host immune system. Loss of immune tolerance is associated with inflammation of the bowel. 

...



Jude Gomila
Jude Gomila approved a suggestion from Golden's AI on 10 Apr 2019 12:58 am
Edits made to:
Article (+15/-15 characters)

Article

Several connections between skin and gut microbiota dysbiosis have been found. AD has been associated with changes in gut microbiota, with lower levels of BifidobacteriumBifidobacterium in the gut than controls. Some studies have shown alterations in gut microbiota composition preceding AD, such as colonization with C. difficile and low Bacteriodetes diversity. In children with AD, whole-metagenome analysis showed depletion of mucin-degrading bacteria such as Akkermansia muciniphila, Ruminococcus gnavus and Lachnospiraceae, bacteria that can influence the immune development. 

Jude Gomila
Jude Gomila approved a suggestion from Golden's AI on 9 Apr 2019 6:38 pm
Edits made to:
Article (+16/-16 characters)

Article

The Canadian Healthy Infant Longitudinal Development (CHILD) study found a lower abundance of bacteria of the genera Lachnospira, Veillonella, FaecalibacteriumFaecalibacterium and Rothia in the gut was associated with asthma later in life and linked mechanistically to reduced faecal short-chain fatty acids (SCFAs). High levels of SCFAs in early life have been shown to be protective against sensitization and asthma later in life. In as US study on a birth cohort, changes in relative abundance of certain microbes in the gut of neonates increased risk of multisensitized atopy and asthma. The children at increased risk had increased pro-inflammatory metabolites including those that induce IL-4 production in CD4+ T cells and decrease abundance of regulatory T cells (Tregs).

Jude Gomila
Jude Gomila approved a suggestion from Golden's AI on 9 Apr 2019 6:38 pm
Edits made to:
Article (+13/-13 characters)

Article

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, StreptococcusStreptococcus, Acinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

Edits on 8 Apr 2019
Meredith Hanel
Meredith Hanel edited on 8 Apr 2019 10:17 pm
Edits made to:
Article (+3/-2 characters)

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The microbiome is the sum of microbes, including bacteria, archaea, viruses, microbial eukaryotes and fungi, and their genomic elements and interactions in their niches. Distinct microbiomes can be found on and in the body of an organism or in the environment. The NIH Common Fund Human Microbiome Project (HMP) is generating resources to facilitate characterization of the human microbiota tofor further understanding of how the microbiome impacts human health and disease. The Earth Microbiome Project aims to characterize all microbial life on earth and understand microbial ecology in different biomes and habitats.

Edits on 5 Apr 2019
Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 5 Apr 2019 4:52 pm
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Article (+13/-13 characters)

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Non-pathogenic organisms affect human health and homeostasis through a variety of mechanisms including metabolism of nutrients and drugs, synthesis of vitamins, defense against pathogens, host bile acid secondary processing, modulation of the immune systemimmune system and modulation of behavior through production of neuroactive compounds.

Edits on 5 Apr 2019
Meredith Hanel
Meredith Hanel edited on 5 Apr 2019 2:42 am
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Article (+646 characters)

Article



Differences between the gut microbes in in babies delivered vaginally versus by caesarean could also be due to confounding factors such as antibiotic administration, labor onset, maternal body weight, maternal diet, gestational age and breastfeeding frequency/duration. Research suggests that differences in intestinal microbe composition between vaginally delivered and caesarean delivered babies resolve after solid foods are introduced. However, the gut microbiome plays an important role in the development of the immune system early in life, which can impact neurodevelopment and risk of metabolic and immune-related diseases later in life. 

Meredith Hanel
Meredith Hanel edited on 5 Apr 2019 2:21 am
Edits made to:
Article (+5/-9 characters)

Article

Most human studies on neonates suggest that contact with maternal and environmental microbes establishes the firstearly colonizers of the infant intestine. Vaginally delivered babies have microbial communities in their intestine dominated by Lactobacillus spp. And Bifidobacterium spp., which are similarly found in the vaginal canal of their mothers. Babies delivered by cesarean section are colonized predominantly by skin microbes with Staphylococcus being the predominant genus. The neonatal gut provides a selective environment, allowing some organisms to colonize and inhibiting others.

Meredith Hanel
Meredith Hanel edited on 5 Apr 2019 2:14 am
Edits made to:
Article (+2214 characters)

Article

The microbiome is the sum of microbes, including bacteria, archaea, viruses, microbial eukaryotes and fungi, and their genomic elements and interactions in their niches. Distinct microbiomes can be found on and in the body of an organism or in the environment. The NIH Common Fund Human Microbiome Project (HMP) is generating resources to facilitate characterization of the human microbiota to further understanding of how the microbiome impacts human health and disease. The Earth Microbiome Project aims to characterize all microbial life on earth and understand microbial ecology in different biomes and habitats.



The field of microbiomics, in which all microorganisms in a community or microbiota are analysed together, uses high-throughput DNA sequencing and RNA sequencing technologies and bioinformatics. Sample DNA is amplified and sequenced and compared to microbial genomic databases to find out the identities and diversity of microbes. Mass spectrometry and nuclear magnetic resonance spectroscopy are used to analyze metabolic interactions between the microbiome and host.

...

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, Acinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

...



Gut microbiome

Most human studies on neonates suggest that contact with maternal and environmental microbes establishes the first colonizers of the infant intestine. Vaginally delivered babies have microbial communities in their intestine dominated by Lactobacillus spp. And Bifidobacterium spp., which are similarly found in the vaginal canal of their mothers. Babies delivered by cesarean section are colonized predominantly by skin microbes with Staphylococcus being the predominant genus. The neonatal gut provides a selective environment, allowing some organisms to colonize and inhibiting others.

Gut microbiome and asthma

The Canadian Healthy Infant Longitudinal Development (CHILD) study found a lower abundance of bacteria of the genera Lachnospira, Veillonella, Faecalibacterium and Rothia in the gut was associated with asthma later in life and linked mechanistically to reduced faecal short-chain fatty acids (SCFAs). High levels of SCFAs in early life have been shown to be protective against sensitization and asthma later in life. In as US study on a birth cohort, changes in relative abundance of certain microbes in the gut of neonates increased risk of multisensitized atopy and asthma. The children at increased risk had increased pro-inflammatory metabolites including those that induce IL-4 production in CD4+ T cells and decrease abundance of regulatory T cells (Tregs).

...

Colonization of airways with Streptococcus, Moraxella or Haemophilus in first 2 months of life has been associated with virus-induced acute respiratory infections and asthma later on. Reduced risk of wheezing at 2 years old was associated with increased abundance of Lactobacillus species at 2 months of age during acute respiratory infection caused by respiratory syncytial virus (RSV). 

Jude Gomila
Jude Gomila approved a suggestion from Golden's AI on 4 Apr 2019 6:29 pm
Edits made to:
Article (+21/-21 characters)

Article

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureusStaphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, Acinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 4 Apr 2019 11:16 am
Edits made to:
Article (+10/-10 characters)

Article

The skin microbiome makeup depends on age, gender, ethnicity, climate, UV exposure and lifestyle factors. The oily, sebaceous gland sites are predominantly inhabited by Propionibacterium species. Staphylococcus species are found in moist microenvironments. Malassezia is a common fungal flora on human skinhuman skin. 

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 4 Apr 2019 11:16 am
Edits made to:
Article (+15/-15 characters)

Article

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, Acinetobacter, CorynebacteriumCorynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis. 

Dawson Sewell
Dawson Sewell approved a suggestion from Golden's AI on 4 Apr 2019 11:16 am
Edits made to:
Article (+26/-26 characters)

Article

Atopic dermatitis (AD), also known as eczema, is associated with dysfunction of the epidermal barrier and linked to Staphylococcus aureus overgrowth and a concomitant decrease in Staphylococcus epidermidisStaphylococcus epidermidis. S. aureus overgrowth is associated with severity of AD and increased allergen sensitization. Antimicrobials that target S. aureus have been shown to reduces AD severity. In contrast, a study on the skin microbiome of infants with AD showed an absence of S. aureus suggesting that colonization with S. aureus may not always predate clinical AD. Members of healthy skin microbiota which are often reduced in AD patients include Propionibacterium, Streptococcus, Acinetobacter, Corynebacterium, Prevotella and Proteobacteria. The fungi, Malassezia are found on healthy skin but increased colonization in AD may contribute to disease pathogenesis.