Potential and active functions in the gut microbiota of a healthy human cohort

Tanca, Alessandro; Abbondio, Marcello; Palomba, Antonio; Fraumene, Cristina; Manghina, Valeria; Cucca, Francesco; Fiorillo, Edoardo; Uzzau, Sergio

doi:10.1186/s40168-017-0293-3

Cited by 136 publications

(136 citation statements)

References 68 publications

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“…In Proteobacteria , Pseudomonas , Parasuterella , Haemophilus , Bilophila , Escherichia and Desulfovibrio were the highest contributors to protein group abundances. Our results are in agreement and further extend previous reports on the phylogenetic diversity of microbial proteins within the human gut (Klaassens et al ., ; Verberkmoes et al ., ; Rooijers et al ., ; Kolmeder et al ., ; Ferrer et al ., ; Perez‐Cobas et al ., ; Juste et al ., ; Brooks et al ., ; Kolmeder et al ., ; Tanca et al ., ; Zwittink et al ., ).…”

Section: Resultsmentioning

confidence: 99%

Gut microbial functional maturation and succession during human early life

Cerdó

Ruiz

Acuña

et al. 2018

Environmental Microbiology

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The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.

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Section: Resultsmentioning

confidence: 99%

Gut microbial functional maturation and succession during human early life

Cerdó

Ruiz

Acuña

et al. 2018

Environmental Microbiology

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“…[20] A previous study has assessed the interaction between atypical antipsychotic (AAP) and gut microbiota in BD patients, and showed gender-specific reduction of species richness in AAPtreated females, which may be associated with metabolic factors. [21,22] Butyrate, one of the main products of colonized microbiota, serves as a major energy source for colonocytes, [23] and plays an important role in immune accommodation, gut barrier regulation, gut metabolism, and energy modulation. Phylum Firmicutes were more abundant in healthy individuals, while greater amounts of Bacteroidetes were found in untreated depressed BD patients, in accordance with a previous study in MDD patients.…”

Section: Discussionmentioning

confidence: 99%

“…[14] Our results demonstrated that the microbial composition in depressed BD patients was clearly different from HCs. [22,24] Butyrate has been reported to be beneficial for many systemic disorders, such as hemoglobinopathy, genetic metabolic diseases, hypercholesterolemia, insulin resistance, and ischemic stroke. [20] Of note, compared to HCs, decreased abundance of various butyrate-producing bacteria was found in untreated BD patients, including genera Roseburia, Faecalibacterium, and Coprococcus.…”

Section: Discussionmentioning

confidence: 99%

Gut Microbiota Changes in Patients with Bipolar Depression

et al. 2019

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This study aims to characterize the gut microbiota in depressed patients with bipolar disorder (BD) compared with healthy controls (HCs), to examine the effects of quetiapine treatment on the microbiota, and to explore the potential of microbiota as a biomarker for BD diagnosis and treatment outcome. Analysis of 16S‐ribosomal RNA gene sequences reveals that gut microbial composition and diversity are significantly different between BD patients and HCs. Phylum Bacteroidetes and Firmicutes are the predominant bacterial communities in BD patients and HCs, respectively. Lower levels of butyrate‐producing bacteria are observed in untreated patients. Microbial composition changes following quetiapine treatment in BD patients. Notably, 30 microbial markers are identified on a random forest model and achieve an area under the curve (AUC) of 0.81 between untreated patients and HCs. Ten microbial markers are identified with the AUC of 0.93 between responder and nonresponder patients. This study characterizes the gut microbiota in BD and is the first to evaluate microbial changes following quetiapine monotherapy. Gut microbiota‐based biomarkers may be helpful in BD diagnosis and predicting treatment outcome, which need further validations.

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“…More recently, a “cell shaving proteomic” approach was used to identify 261 cell surface‐associated proteins of G. vaginalis in culture . This technology has several advantages as the metaproteome reflects the actual protein output, which may diverge from measures of bacterial community structure defined by amplicon sequencing, gene content (SMS) or metatranscriptomes .…”

Section: Introductionmentioning

confidence: 99%

The genital tract and rectal microbiomes: their role in HIV susceptibility and prevention in women

et al. 2019

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Introduction Young women in sub‐Saharan Africa are disproportionately affected by HIV, accounting for 25% of all new infections in 2017. Several behavioural and biological factors are known to impact a young woman's vulnerability for acquiring HIV. One key, but lesser understood, biological factor impacting vulnerability is the vaginal microbiome. This review describes the vaginal microbiome and examines its alterations, its influence on HIV acquisition as well as the efficacy of HIV prevention technologies, the role of the rectal microbiome in HIV acquisition, advances in technologies to study the microbiome and some future research directions. Discussion Although the composition of each woman's vaginal microbiome is unique, a microbiome dominated by Lactobacillus species is generally associated with a “healthy” vagina. Disturbances in the vaginal microbiota, characterized by a shift from a low‐diversity, Lactobacillus ‐dominant state to a high‐diversity non‐ Lactobacillus ‐dominant state, have been shown to be associated with a range of adverse reproductive health outcomes, including increasing the risk of genital inflammation and HIV acquisition. Gardnerella vaginalis and Prevotella bivia have been shown to contribute to both HIV risk and genital inflammation. In addition to impacting HIV risk, the composition of the vaginal microbiome affects the vaginal concentrations of some antiretroviral drugs, particularly those administered intravaginally, and thereby their efficacy as pre‐exposure prophylaxis (PrEP) for HIV prevention. Although the role of rectal microbiota in HIV acquisition in women is less well understood, the composition of this compartment's microbiome, particularly the presence of species of bacteria from the Prevotellaceae family likely contribute to HIV acquisition. Advances in technologies have facilitated the study of the genital microbiome's structure and function. While next‐generation sequencing advanced knowledge of the diversity and complexity of the vaginal microbiome, the emerging field of metaproteomics, which provides important information on vaginal bacterial community structure, diversity and function, is further shedding light on functionality of the vaginal microbiome and its relationship with bacterial vaginosis (BV), as well as antiretroviral PrEP efficacy. Conclusions A better understanding of the composition, structure and function of the microbiome is needed to identify opportunities to alter the vaginal microbiome and prevent BV and reduce the risk of HIV acquisition.

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Potential and active functions in the gut microbiota of a healthy human cohort

Cited by 136 publications

References 68 publications

Gut microbial functional maturation and succession during human early life

Gut microbial functional maturation and succession during human early life

Gut Microbiota Changes in Patients with Bipolar Depression

The genital tract and rectal microbiomes: their role in HIV susceptibility and prevention in women

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