Fehmida Bibi

Culture of previously uncultured members of the human gut microbiota by culturomics

Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism1. The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms2. We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization–time of flight and 16S rRNA for identification2. Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies3–5. We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut.

Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics

The human gut flora is currently widely characterised using molecular techniques. Microbial culturomics (large-scale culture conditions with identification of colonies using MALDI-TOF or 16S rRNA) is part of the rebirth of bacterial culture that was initiated by environmental microbiologists for the design of axenic culture for intracellular bacteria in clinical microbiology. Culturomics was performed on four stool samples from patients treated with large-scale antibiotics to assess the diversity of their gut flora in comparison with other culture-dependent studies. Pyrosequencing of the V6 region was also performed and was compared with a control group. Gut richness was also estimated by bacterial counting after microscopic observation. In total, 77 culture conditions were tested and 32,000 different colonies were generated; 190 bacterial species were identified, with 9 species that had not been isolated from the human gut before this study, 7 newly described in humans and 8 completely new species. A dramatic reduction in diversity was observed for two of the four stool samples for which antibiotic treatment was prolonged and uninterrupted. The total number of bacteria was generally preserved, suggesting that the original population was replaced but was sustained in size. Discordances between culture and pyrosequencing biodiversity biomarkers highlight the depth of bias of molecular studies. Stool samples studied showed a dramatic reduction in bacterial diversity. Considering the variable antibiotic concentration in the gut, this reduction in the number of species is possibly linked to the production of bacteriocin in the upper digestive tract by specific bacteria, such as Lactobacillus spp.

Role of gut microbiota in obesity, type 2 diabetes and Alzheimer's disease.

In recent years, there is a growing interest in research to investigate the importance of gut microbiome in health and diseases. This opens a new area of research for the role of microbial flora of the human gut in inflammation, energy homeostasis, pathogenesis of obesity and other associated disorders. Recent studies propose association of the gut microbiome with development of obesity and metabolic syndromes, such as type 2 diabetes mellitus (T2DM). The T2DM is a metabolic disease that is mainly caused by obesity-linked insulin resistance. The vascular effects of obesity appears to play a role in the development of Alzheimers disease (AD) that is one of the rapidly growing diseases of a late stage of life all over the world. Studies from both humans and mice models have been demonstrated the engagement of gut microbial flora in the pathogenesis of obesity and host metabolism. The aim of this review is to discuss the current findings that may explain the cascade of gut microbial flora participation in the development of obesity, T2DM and further initiation of AD. In addition, the available data regarding the mechanisms that have been proposed to elucidate the role of gut microbiota in weight gain and possible cause of T2DM and AD have been examined.

Diversity and Characterization of Endophytic Bacteria Associated with Tidal Flat Plants and their Antagonistic Effects on Oomycetous Plant Pathogens

Endophytic bacterial communities of tidal flat plants antagonistic to oomycete plant pathogens were studied by the isolation of 256 root colonizing endophytic bacteria from surface-disinfected root tissues of six plants (Rosa rugosa, Suaeda maritima, Vitex rotundifolia, Carex scabrifolia, Glehnia littoralis and Elymus mollis) growing in a tidal flat area of Namhae Island, Korea. To understand the antagonistic potential, an in vitro antagonistic assay was performed to characterize and identify strains that were antagonistic to the oomycete plant pathogens Phytophthora capsici and Pythium ultimum from the total population. Nine percent of the total number of isolated bacteria exhibited in vitro inhibitory activity against target plant pathogenic oomycetes. Taxonomic and phylogenetic placement of the antagonistic bacteria was investigated by analysis of the 16S rRNA gene sequences. The sequence analysis classified the antagonistic strains into four major classes of the domain bacteria (Firmicutes, α-Proteobacteria, γ-Proteobacteria and Actinomycetes) and 10 different genera. Further production of secondary metabolites, hydrolytic enzymes and plant growth promoting traits were determined for the putative new species of antagonistic endophytic bacteria. These new strains could not be identified as known species of α-Proteobacteria, and so may represent novel bacterial taxa. The unexpected high antagonistic bacterial diversity associated with the tidal flat plants may be indicative of their importance in tidal flat plants as a promising source of novel antimicrobial compounds and biocontrol agents.

Comparison of the gut microbiota of people in France and Saudi Arabia

Background/Objectives:The gut microbiota contributes to energy acquisition from food, and changes in the gut microbiome are associated with obesity. The eating habits of Saudis are much different than those of Europeans, and our objective was to compare the fecal microbiota of obese and normal weight Saudis and French.Subjects/Methods:Illumina MiSeq deep sequencing was used to test the gut microbiota of 9 normal weight and 9 obese individuals from Saudi Arabia and 16 normal weight and 12 obese individuals from France.Results:Obese French possessed significantly more relative Proteobacteria (P=0.002) and Bacteroidetes (P=0.05) and had lower richness and biodiversity at all the operational taxonomic unit (OTU) cutoffs (P<0.05) than normal weight French. Obese Saudis possessed significantly more Firmicutes (P=0.001) without a difference in richness (P=0.2) and biodiversity (P=0.3) compared with normal weight Saudis. We found a common bacterial species core of 23 species existing in ⩾50% of obese and normal weight Saudis and 29 species in ⩾50% of obese and normal weight French. Actinomyces odontolyticus, Escherichia coli and Ruminococcus obeum were present in at least 50% of all individuals tested. French individuals had significantly higher richness and biodiversity compared with Saudis at all the OTU cutoffs (P<0.05).Conclusion:Microbiota differences between obese and normal weight French were not similar to those between obese and normal weight Saudis. The studies of different populations can result in contrasting data regarding the associations of the gut microbiota and obesity.

Link Between Chronic Bacterial Inflammation and Alzheimer Disease

Alzheimers disease (AD) is a degenerative disease of brain that is associated with dementia, brain atrophy, accumulation of hyperphosphorylated tau protein and amyloid-beta peptide in hippocampus and cortex region of the brain. The development of AD is a multifactorial process that may also involve infection with bacterial pathogens. Recent studies suggest that bacteria including spirochetes have the potential to initiate cascade of events, leading to inflammatory condition of the central nervous system. Bacteria and spirochetes are activators of proinflammatory cytokines, generate free radicals, nitric oxide and further induction of apoptosis. Infection with these microbes may be considered as a risk factor for pathophysiology of AD or to cognitive changes. Recent studies have revealed that exposure to these microorganisms induces Aβ accumulation and tau protein phosphorylation, and chronic infections with these pathogenic bacteria can possibly contribute to progression of AD. In this article, we update and review the role of bacteria in the pathogenesis of AD resulting from initiation of cascade events in chronic inflammations and amyloidogenesis. Controlling these chronic infections with antibacterial or anti-inflammatory drugs will allow preventing inflammation, a risk factor for AD.

Paper money and coins as potential vectors of transmissible disease.

Paper currency and coins may be a public health risk when associated with the simultaneous handling of food and could lead to the spread of nosocomial infections. Banknotes recovered from hospitals may be highly contaminated by Staphylococcus aureus. Salmonella species, Escherichia coli and S. aureus are commonly isolated from banknotes from food outlets. Laboratory simulations revealed that methicillin-resistant S. aureus can easily survive on coins, whereas E. coli, Salmonella species and viruses, including human influenza virus, Norovirus, Rhinovirus, hepatitis A virus, and Rotavirus, can be transmitted through hand contact. Large-scale, 16S rRNA, metagenomic studies and culturomics have the capacity to dramatically expand the known diversity of bacteria and viruses on money and fomites. This review summarizes the latest research on the potential of paper currency and coins to serve as sources of pathogenic agents.

Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.

BackgroundSaudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands.ResultsIn general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples.ConclusionsBacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov.

Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.

Gut microbiome and dietary patterns in different Saudi populations and monkeys

Host genetics, environment, lifestyle and proximity between hosts strongly influence the composition of the gut microbiome. To investigate the association of dietary variables with the gut microbiota, we used 16S rDNA sequencing to test the fecal microbiome of Bedouins and urban Saudis and we compared it to the gut microbiome of baboons living in close contact with Bedouins and eating their leftovers. We also analyzed fermented dairy products commonly consumed by Bedouins in order to investigate their impact on the gut microbiome of this population. We found that the gut microbiomes of westernized urban Saudis had significantly lower richness and biodiversity than the traditional Bedouin population. The gut microbiomes of baboons were more similar to that of Bedouins compared to urban Saudis, probably due the dietary overlap between baboons and Bedouins. Moreover, we found clusters that were compositionally similar to clusters identified in humans and baboons, characterized by differences in Acinetobacter, Turicibacter and Collinsella. The fermented food presented significantly more bacteria genera common to the gut microbiome of Bedouins compared to urban Saudis. These results support the hypothesis that dietary habits influence the composition of the gut microbiome.