Cardiovascular disease (CVD) remains the leading cause of death globally, responsible for an estimated 17.9 million deaths annually. Traditional screening and diagnostic tests often fail to identify those at risk until a late stage, it is therefore essential to develop new predictive tests to enable diagnosis at an earlier stage to facilitate preventative treatments. Recently, many studies have shown that high levels of circulating Trimethylamine N-oxide (TMAO) are indicative of an increased risk of CVD. Through the analysis of TMAO levels it was found patients whose TMAO level was in the 4th quartile had a 2.29 fold increase of major adverse cardiac events (MACE) over patients whose level was in the 1st quartile (p < 0.05). These studies have also demonstrated the role of the gut microbiome in the formation of TMAO. This review will provide an overview of the role of the gut microbiome and explore the evidence linking TMAO and CVD.
•The vaginal microbiomes of recurrent BV patients differ significantly from healthy controls.•Metronidazole temporarily reinstates healthy vaginal flora of recurrent BV patients.•Oral Metronidazole is insufficient long-term treatment for recurrent BV.•Future research into alternative treatment and cure for BV warranted.
•193 school-aged children with low and 183 with high screen viewing (sitting) times.•Saliva microbiota diversity was higher in children with low screen times.•Microbiota composition differed between the screen time groups.•Ten taxonomic groups were differentially abundant between the screen time groups.•Five metabolic pathways were differentially present between the screen time groups.
The cervicovaginal microbiome consists of community state types (CSTs) I-V. Several studies have reported positive correlations between health issues such as bacterial vaginosis (BV), acquisition of sexually transmitted infections (STIs), preterm labour and CST IV. The cervicovaginal microbiome in Afro-Caribbean women has never been characterized. Hence, this study aimed to determine the composition, CST, microbial function and resistome of the cervicovaginal microbiome in a cohort of Afro-Caribbean women using targeted (16S rRNA V4) and whole genome shotgun metagenomics. CST IV predominated in this ethnic group, with Prevotella (13.91 %) being the most abundant genus followed by Gardnerella (12.14 %). The relative abundance for Lactobacillus was 9.37 %. The most abundant species for Prevotella and Lactobacillus were P. timonensis (5.00 %) and L. iners (7.00 %), respectively. Taxa with significant nucleotide similarity to the less virulent culture collection strain G. vaginalis 409–05 (8.14 %) were more abundant than G. vaginalis ATCC 14019 (4.00 %) in this group that was asymptomatic of BV. Functional profiling revealed a high abundance of biological processes (such as flagellum-dependent cell motility, cell adhesion and quorum sensing) associated with biofilm activity. In the resistome, 2,753 predicted antimicrobial resistance (AMR) genes consisting of 28 types (mostly tet and Emr; relative abundance 52.94 % and 16.18 %, respectively) that can potentially confer resistance to tetracyclines and the macrolide-lincosamide streptogramin B group were identified. Theoretically, these AMR genes can impact the effectiveness of antibiotics commonly used in the treatment of STIs and BV. This study is the first to provide insight into the cervicovaginal microbiome and its resistome in Afro-Caribbean women.
The role of the human gut phageome (HGP) for a healthy gut microbiome is not well-established. This study aims to identify phages based on Reduced Metagenome Sequencing (RMS) fragments from an Indian mother and child cohort. For this study, fecal samples were collected from 17 mother-infant pairs at Nishanth Hospital, Tamil Nadu, India. RMS data analysis and shotgun sequencing approaches were used to assemble and identify the genome fragments. Out of the 156,926 RMS fragments, 434 were classified as bacteriophages by Kraken 2. Mapping of virus sequences in NCBI and de novo assembly with subsequent taxonomic assignment revealed 41 different phage species. The prevalence (>50%) of three bacteriophages was observed in mother and child; overall four phages were more prevalent in the mothers while one phage was more prevalent in the children. Even at the species level, mothers were found to have more diverse phage species than children. No significant association was observed for mother–child sharing of phages. This study highlights the prevalence of Caudovirales phages in healthy HGP and also the use of the RMS approach to study the phageome composition.
BACKGROUND:The oral microbiome is a complex assembly of microbial species, whose constituents can tilt the balance towards progression of oral disease or sustained health. Recently we identified sex-specific differences in the salivary microbiome contained within caries-active and caries-free children. In this study, we sought to ascertain if adjunctive dental therapies, including povidone iodine and chlorhexidine, were effective in shifting the cariogenic microbiome from dysbiosis to non-cariogenic health.DESIGN:We recruited young children (ages 2-12 years) to enter five enrollment groups, with each group (N = 9-30 participants/group) receiving caries restorative and/or adjunctive therapies, either singularly or in combination (OHSU IRB #6535). Saliva specimens were collected pre- and post-treatment (4-8 weeks) of caries preventive measures, and oral microbiota were identified using next generation sequencing (HOMINGS, Forsyth Institute, Cambridge, MA).RESULTS:With the use of multi-dimensional scaling plots, support vector machine learning, odds ratio analysis, and other statistical methods, we have determined that treatment with povidone iodine can shift the composition of the salivary cariogenic microbiome to include higher proportions of aerobic microorganisms, such as Stentrophomonas maltophila, as well as non-cariogenic, anaerobic microorganisms including Poryphyromonas and Fusobacterium species.CONCLUSION:We have identified microorganisms that are associated with caries-active children and have determined that povidone iodine is an effective adjunctive therapy that has the potential to shift the composition of the cariogenic microbiome to one more closely aligned with non-cariogenic health.
•Investigation of gut microbiome composition and diversity with respect to human personality.•Analyses targeted bacterial genera linked to behaviour in animal and human psychiatric studies.•Bacterial genera were modelled (using negative binomial regression) with respect to personality.•Genera linked to autism are also related to social behaviour in the general population.•Sociability is associated with higher diversity, and anxiety and stress with reduced diversity.
Patients colonized with antibiotic resistant bacteria are at risk of infections and spontaneous decolonization delays are highly variable between patients. The management of these patients is therefore time-consuming; requires patient isolation, and cohort policies. Fecal microbiota transplantation (FMT) has been used with the aim of shortening this gut colonization. Here, we proposed a comprehensive literature review on FMT utilization for gut antibiotics resistant bacteria decolonization. After literature research through Pubmed indexed for MEDLINE, we analyzed 23 studies with description of FMT utilization and analyze of gut decolonization. In total, the data involved 197 patients, 153 of whom underwent FMT. Overall, 66.7% (102/153) of the patients were decolonized after FMT. However, we noticed a lot of interpretation bias, such as variation in colonization definition and high disparities in FMT administration modalities. Two disparities were of special interest: repeated FMT seems to increase the effectiveness of decolonization, and gut decolonization with antibiotics before FMT was proposed by some authors, but with too few studies to draw a conclusion. Overall, the use of FMT is a promising perspective for intestinal decolonization, but it requires greater standardization.
Vaginal microbiota has been postulated as a key contributor to the disproportionately higher HIV acquisition risk in women. The commensal bacterial communities in the vaginal tract have been implicated in HIV pathogenesis, with strict anaerobes such as Gardnerella and Prevotella causing inflammation and increased frequency of HIV target cells. Young African women are up to six times more likely to be infected with HIV than their male counterparts. The underlying biological mechanisms for increased susceptibility to HIV infection are not fully known, particularly among pregnant women who are also at risk of transmitting the infection to their unborn babies.
The infection process of bacterial gastroenteritis often relies on the initial binding of toxins to carbohydrate receptors on host cells. We screened the human gut microbiota for microorganisms naturally expressing toxin-binding carbohydrate structures. Out of stool samples from four healthy adult donors, we isolated bacterial strains specifically binding the cholera toxin and the heat labile toxin. These results suggest a new mechanism by which the microbiome may shape people’s individual sensitivity to gastrointestinal infections. This study may also pave the way for the development of non-antibiotic microbiome based strategies to treat and prevent gastrointestinal infections.
•More than 320 diarrheagenic E. coli (DEC) and 62 Salmonella isolates were recovered from stool specimens collected from diarrheal patients within the Amathole District Municipality, Eastern Cape, South Africa.•More than 3 three diarrheagenic E. coli pathovars were detected and confirmed from diarrheal specimens.•Bacterial pathogens co-infections presented in the present study, suggest a noteworthy therapeutic and subsequently worrisome public health concern.
Enterococci are members of human gut microbiota which their colonization has been demonstrated even before birth. This indicates their importance in infant health. As this population is dynamic and varies with age, this study was designed to assess and compare the antibacterial effects of enterococci from breast-fed infants and those from adults. Fecal isolates of enterococci were isolated from infants and healthy adults and were identified to the species level by phenotypic and genotypic methods. Further, they were evaluated for their potential to exert antibacterial effect against ten standard bacterial strains using bilayer spot test. Of a total of eighty-nine recovered enterococcal isolates, Enterococcus faecium and E. faecalis were the most common species (98%) and showed inhibitory effects at least against one indicator strain. Comparison between isolates from two studied groups showed that isolates from neonates introduced significantly higher growth inhibitory effects against six indicator strains (P < 0.05) and these effects were frequently attributable to E. faecium isolates. In addition, the highest growth inhibitory effect was observed against Listeria monocytogenes. Antimicrobial effects of enterococci in human microbiota change during time. The beneficial role of these organisms within the neonatal period suggests the potential of enterococci from breast-fed infants for probiotic application.
Coronavirus disease 2019 (COVID-19) is a rapidly emerging disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease begins as an infection of lungs, which is self-limiting in the majority of infections; however, some develop severe respiratory distress and organ failures. Lung microbiome, though neglected previously have received interest recently because of its association with several respiratory diseases and immunity. Lung microbiome can modify the risk and consequences of COVID-19 disease by activating an innate and adaptive immune response. In this review, we examine the current evidence on COVID-19 disease and lung microbiome, and how lung microbiome can affect SARS-CoV-2 infection and the outcomes of this disease. To date there is no direct evidence from human or animal studies on the role of lung microbiome in modifying COVID-19 disease; however, related studies support that microbiome can play an essential role in developing immunity against viral infections. Future studies need to be undertaken to find the relationship between lung microbiome and COVID-19 disease.
•Clostridioides difficile infection is one of the most frequently nosocomial diseases.•Faecal microbiota transplantation is safe and inexpensive therapeutic procedure.•Transferred donor stool can restore the natural diversity of intestinal microbiota.•Advanced patient age was the only significant risk factor for treatment failure.
We read with interest a work of the Gordon team reporting a gut microbiota immaturity in severe acute malnutrition. However, almost all gut microbes are found in colostrum and breast milk, including methanogenic Archaea. These Archaea are detected in baby’s stomach and in 40% healthy control children but are lost in severe acute malnutrition. Bifidobacterium breve and Bifidobacterium longum are other exceptions to immaturity. These errors are critical because they are a key to treat and cure these children. We argue that milk probiotics including Bifidobacterium, Lactobacillus and Archaea could be the next revolution in the management of malnutrition.
An increasing number of scientists are turning to the microbiota to understand and/or explain the origin of various human metabolic or inflammatory diseases. Oxygen-intolerant bacteria represent the major population of the human intestinal microbiota. Their isolation is often difficult or even fastidious. The number of studies showing their beneficial role in human health is growing exponentially. Faecalibacterium prausnitzii and Akkermansia muciniphila are abundantly represented in healthy intestinal microbiota and their imbalance is positively correlated with inflammatory diseases and metabolic disorders (obesity, diabetes, cancers). Their use as probiotics presents very promising results in restoring the balance of microbial flora but also in the treatment of certain pathological conditions. The Christensenellaceae family has recently emerged as a hereditary taxon and studies have shown that its abundance is positively correlated with leanness and controls obesity in recipient mice. Here, we report the different culture strategies and techniques used for their isolation; the role of antioxidants in the survival of these oxygen-sensitive species in clinical sample and their maintenance in culture isolates.
Autism Spectrum Disorder (ASD) is a collection of neurodevelopmental disorders defined by core deficits, including impaired communication, reciprocal social interaction, and stereotyped and repetitive patterns of behaviors. The salivary microbiota may serve as important indicators of oral and systemic health. In this pilot study, we identify components of the salivary microbiome in children with ASD. Saliva specimens were collected from 11 children with ASD (mean age: 10.68 years) and from 10 typically-developing individuals. Microbial DNA was extracted and utilized as templates for PCR amplification with V3-V4 16S rDNA-specific primers and high-throughput MiSeq sequencing. Taxonomic operational unit analyses and salivary microbiota profiles were conducted by LC Sciences (Houston TX); individual microbial species were further compared between children with ASD and typically-developing individuals. Rothia species were found to be statistically more prevalent in children with ASD in comparison to typically-developing children (12.2-fold change; FDR p-value = 0.031). Alternately, Megasphaera, Moraxella, Neisseria, and Gemella species were all found at significantly higher levels in typically-developing children than children with ASD, displaying 39.2-, 31.9-, 18.8- and 14.0-fold differences, respectively (all with FDR p-values < 0.011). In boys with ASD, Moraxella and Neisseria species were found at significantly-higher levels compared to typically-developing counterparts, exhibiting 42.36- and 28.62-fold differences, respectively (FDR p-values of 0.011 and 0.0004). Understanding the salivary microbiome in children with autism can lead to improved management of oral health and precision treatment planning. In addition, practitioners may be able to modify the oral microbiome as therapeutic regimens for ASD and other oral diseases.
The human gastrointestinal tract is home to the most diverse microbial ecosystem in the human body and is made up of bacteria, viruses and eukarya. Collectively known as the gut microbiota, our knowledge of these microbial communities has historically been restricted by the relative limitations of culturing techniques. However, the recent development and utilisation of next-generation sequencing techniques has enhanced our understanding of its structure, diversity and function.
Neurodegenerative diseases are estimated to afflict hundreds of thousands of Americans with vastly more worldwide. The etiologies of amyotrophic lateral sclerosis (ALS) and multiple sclerosis (MS) have yet to be established. Previous studies have suggested an association of these diseases with viruses, bacteria, and eukaryotic microbes, no new therapies have been forthcoming. High-throughput DNA sequencing has enabled the comprehensive analysis of microbial DNA profiles in diseased populations. To date, no amplicon-based next-generation DNA sequencing prokaryotic and eukaryotic community profiling studies have been completed for these diseases. Analysis of peripheral blood samples from control participants as well as ALS and MS participants was used to characterize the hematologic population of microbial DNA. Categorical and multivariate analysis with control for multiple comparisons and aged matched controls revealed differences in microbial DNA contribution in ALS patients compared to others. Notably, sequences that belonging to Ochrophyta were enriched in ALS patient samples. Mechanisms underlying this association, the role of microbial DNA sequences, and the development or progression of ALS may become a fertile subject of inquiry.
Bacteria that colonize the vaginal microbiota of women play an important role in health and homeostasis. Disruption of the proportion of bacteria predisposes to dysbiosis like bacterial vaginosis or severe gynecological conditions such as preterm birth, pelvic inflammatory disease and also sexually transmitted diseases. Knowledge about normal and abnormal vaginal microbiota has become a little clearer in recent years. Culture techniques have made it possible to isolate and describe many bacterial species, whereas molecular methods have highlighted the limits of culture by showing that the vagina was a complex ecosystem containing a wide range of non-cultured or difficult-to-identify bacteria. Based on an exhaustive review of the scientific literature, we built the repertoire of all the bacteria found using culture-based and/or independent methods on the human vagina. So, whether they are valid or not, we inventoried 581 bacteria identified in the human vagina distributed into 10 taxa, mainly in the phyla of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria with 206 distinct genera classified in 96 different families. This repertoire is essential for microbiologists and clinicians and represents the starting point for a Vaginal Microbiome Project such a project aimed to map the human vaginal microbiota, to better understand the dysbioses or infections caused by its imbalance in order to offer more appropriate treatments.
