Effect of antibiotics on the human microbiome: a systematic review

Zyl, Kristien Nel Van; Matukane,; Hamman, Bianca; Whitelaw, Andrew; Newton-Foot, Mae

doi:10.1016/j.ijantimicag.2021.106502

Cited by 33 publications

(22 citation statements)

References 112 publications

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“…Antibiotic interference in the lactation period resulted in increased abundance and diversity of microbiota in the stomach and ileum mucus. Previous studies on antibiotic-exposed microbiota have found that the α-diversity was reduced in stool samples after the intervention ( 47 , 48 ), while the host microbiota in different GI parts could have different proliferative capacities after antibiotic treatment ( 49 ). Moreover, it can be varied with different antibiotic types ( 47 , 49 ).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies on antibiotic-exposed microbiota have found that the α-diversity was reduced in stool samples after the intervention ( 47 , 48 ), while the host microbiota in different GI parts could have different proliferative capacities after antibiotic treatment ( 49 ). Moreover, it can be varied with different antibiotic types ( 47 , 49 ). Long-term use of antibiotics can cause the decrease of dominant flora and overgrowth of foreign flora or nonpathovar flora, which may result in a further increase in α-diversity ( 50 , 51 ).…”

Section: Discussionmentioning

confidence: 99%

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Development of Early-Life Gastrointestinal Microbiota in the Presence of Antibiotics Alters the Severity of Acute DSS-Induced Colitis in Mice

Ren

Zhang

et al. 2022

Microbiol Spectr

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This study investigated resident microbiota in the whole gastrointestinal (GI) tract to explore gut microbiota development in early life and found that early-life antibiotic exposure exacerbated alterations in gut microbiota and murine dextran sulfate sodium (DSS)-induced colitis. Furthermore, the presence of bacteria in the GI tract of mice before birth and the importance of the lactation period in GI microbiota development were confirmed.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Development of Early-Life Gastrointestinal Microbiota in the Presence of Antibiotics Alters the Severity of Acute DSS-Induced Colitis in Mice

Ren

Zhang

et al. 2022

Microbiol Spectr

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“…Of all antibiotics, β-Lactam antibiotics were most commonly used in our cohort. Prospective cohort studies revealed that Shannon biodiversity index was decreased during amoxicillin treatment and was subject to further reduction in the following 6 months’ time period ( Menon et al, 2019 ; Monroy-Pérez et al, 2020 ; Nel Van Zyl et al, 2022 ). The density of Neisseria, Streptococcus and Veillonella strains in the oral cavity was also reported to decrease during treatment with amoxicillin ( Larsson Wexell et al, 2016 ; Moraes et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Cultivable oral bacteriota dysbiosis in mechanically ventilated COVID-19 patients

Gregorczyk-Maga

Fiema²,

Michal³

et al. 2022

Front. Microbiol.

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Potential interactions between the SARS-CoV-2 virus and the human oral microbiota are currently investigated widely. Patients with COVID-19 requiring mechanical ventilation in an intensive care unit (ICU) setting are at high risk of developing severe complications, including ventilator-associated pneumonia, thus making oral health management important. The aim of this study was to evaluate the oral health status and assess the dysbiosis of cultivable oral bacteriota in COVID-19 patients hospitalized in an ICU with acute respiratory distress within 36 h following intubation. In this prospective cohort study, we recruited 56 adult COVID-19 patients that qualified for mechanical ventilation in the Temporary ICU for COVID-19 Patients of the University Hospital in Krakow. On admission to the ICU, oral health of patients was assessed using the modified Beck Oral Assessment Score (BOAS). Four oral habitats were sampled, namely the buccal mucosa, tongue, buccal dental surface and gingival pocket. Microorganisms were identified by MALDI/TOF mass spectrometry. The mean age of the study population was 66.5 ± 12.7 years, there were 24 (42.9%) females. All patients included in this study were intubated and ventilated in the ICU, with a corresponding high mortality rate (76.8%). On admission to ICU, 76.8% subjects scored 11–20 on the BOAS scale (median 12 [IQR 10–14]), indicating moderate or severe dysfunction of oral health. Potentially pathogenic bacteria were identified in the oral microbiota samples, including Acinetobacter baumannii, Enterococcus faecalis, Escherichia coli and Klebsiella pneumoniae in 23.2%, 39.3%, 17.9%, and 19.6% of patients, respectively. Lactobacillus spp. were present in 57.1% subjects. The mean CFU counts of all bacteria strains in dental brushes were 9.3E+5 (1.4E+6) and in gingival pockets 7.6E+5 (1.4E+6). The highest CFU counts were observed for Enterococcus spp. and, Lactobacillus spp., although these did not differ significantly from CFU counts of Streptococcus spp. and Staphylococcus spp. In this report we comprehensively characterized the oral health condition and cultivable oral bacteriota in COVID-19 patients hospitalized in an ICU with acute respiratory distress within 36 h following intubation. The oral bacteriota showed significant qualitative and quantitative dysbiosis. Hospitalization in an ICU and mechanical ventilation are important factors leading to oral dysbiosis in SARS-CoV-2 patients.

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“…Evidence also describes antibiotic use to affect microbiome at other anatomical sites, and associated with diseases including affected lipid metabolism, inflammation, and auto-immune conditions [50][51][52] . The patient variability in treatment exposure to antibiotics and / or corticosteroids treatment, and duration from last treatment to sample collection will affect systemic microbiome, and could explain some of the interpatient metagenomic variability 51 .…”

Section: Streptococcus Pyogenes Escherichia Coli Bacteroides Species ...mentioning

confidence: 99%

16S rRNA sequencing for profiling microbial communities in idiopathic granulomatous mastitis

Ong

Sim

et al. 2022

Preprint

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Background: Idiopathic granulomatous mastitis (IGM) is a rare, chronic, and benign inflammatory breast disease with ambiguous aetiology. Contrastingly, lactational mastitis (LM) is commonly diagnosed in breastfeeding women. To investigate IGM aetiology, we profiled the microbial flora of pus and skin in IGM and LM patients. Methods: IGM patients were recruited from 2018 to 2020; LM patients were recruited as controls. 16S rRNA sequencing libraries were constructed from 16S rRNA gene amplified from total DNA extracted from pus and skin swabs. Metagenomic analysis was conducted using modified microbiome abundance analysis-suite customised R-resource for paired pus and skin samples. Microbiome multivariable association analyses were performed using linear models. Results: 21 IGM and 3 LM paired pus and skin samples underwent metagenomic analysis. Bray-Curtis ecological dissimilarity distance showed dissimilarity across four sample types (IGM-pus, IGM-skin, LM-pus, LM-skin; PERMANOVA, p<0.001). No characteristic dominant genus was observed across IGM samples. IGM pus samples were more diverse than corresponding IGM skin samples (Shannon and Simpson index; Wilcoxon paired signed-rank tests, p=0.022 and p=0.07). Corynebacterium kroppenstedtii, reportedly associated with IGM in literature, was higher in IGM pus samples than paired skin sample (Wilcoxon, p=0.022). Three other species and nineteen genera were statistically significant in paired IGM pus-skin comparison after antibiotic treatment adjustment, and multiple comparisons correction. Conclusions: Microbial profiles are unique between IGM and LM patients. Inter-patient variability and polymicrobial IGM pus samples cannot implicate specific genus or species as an infectious cause for IGM.

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Effect of antibiotics on the human microbiome: a systematic review

Cited by 33 publications

References 112 publications

Development of Early-Life Gastrointestinal Microbiota in the Presence of Antibiotics Alters the Severity of Acute DSS-Induced Colitis in Mice

Development of Early-Life Gastrointestinal Microbiota in the Presence of Antibiotics Alters the Severity of Acute DSS-Induced Colitis in Mice

Cultivable oral bacteriota dysbiosis in mechanically ventilated COVID-19 patients

16S rRNA sequencing for profiling microbial communities in idiopathic granulomatous mastitis

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