The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.

/pdf/metagenomic-biomarker-discovery-and-explanation-x530ilzkca.pdf

Metagenomic biomarker discovery and explanation

The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

/pdf/structure-function-and-diversity-of-the-healthy-human-4mecpxyl8r.pdf

Structure, function and diversity of the healthy human microbiome

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.

/pdf/the-human-microbiome-project-1armeyuv2c.pdf

The human microbiome project.

https://www.cell.com/cell/pdf/S0092-8674(15)01267-2.pdf

Winning the Microbial Battle, but Not the War

Background The gut microbiome is altered in several neurologic disorders including Parkinson’s disease (PD). Objectives Profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression. Methods Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n=48, n=47, respectively), environmental Household Controls (HC, n=29, n=30), and community Population Controls (PC, n=41, n=49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic datasets from two previous studies in Germany and China to determine generalizable microbiome features. Results The gut microbiome in PD shows significant alterations in community composition. Robust taxonomic alterations include depletion of putative “beneficial” gut commensals Faecalibacterium prausnitzii and Eubacterium and Roseburia species, and increased abundance of Akkermansia muciniphila and Bifidobacterium species. Pathway enrichment analysis and metabolic potential, constructed from microbial gene abundance, revealed disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism. These global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted inter-community signaling. Conclusions A metagenomic meta-analysis of PD shows consistent and novel alterations in taxonomic representation, functional metabolic potential, and microbial gene abundance across four independent studies from three continents. These data reveal stereotypic changes in the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research.

https://authors.library.caltech.edu/115803/1/2022.07.20.500694v1.full.pdf

Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome

Environmentally-induced alterations in the commensal microbiome have been implicated in
the increasing prevalence of food allergy. We found that antibiotic treatment of neonatal
mice leads to reduced proportions of regulatory T cells (Tregs) in the colonic lamina
propria(LP), impaired production of intestinal IgA, and elevated peanut (PN) specific
IgE/IgG1 in response to sensitization. Selective colonization of gnotobiotic mice linked the
Treg/IgA inducing capacity to a consortium of bacteria within the Clostridia class.
Introduction of either a conventional SPF microbiota or a mixture of Clostridia strains to
antibiotic-treated mice restored the Treg and IgA compartments and blocked the induction
of a food allergic response. Clostridia colonized gnotobiotic mice displayed increased
expression of IL-23 and IL-22 in the colonic LP compartment and the induction of
anti-microbial REG3β expression in the epithelium. Collectively, these results suggest that
the maintenance of oral tolerance to dietary antigens relies on bacterial populations that
induce a barrier protective response, which includes activation of the IL-23/IL22 axis and
the expansion of intestinal Tregs and IgA secreting B cells. Our findings hold promise for
the development of approaches to prevent or treat food allergy based on modulation of the
composition of intestinal microbiota.

Commensal bacteria induce a barrier protective response to prevent sensitization to food allergens

Category: Microbiome
Background: An essential function of the gut microbiota is to
regulate immune responses, including T lymphocyte functions in
health and disease.
Objectives: We hypothesized that gut microbiota contribute to the
pathogenesis of MS.
Methods: We analyzed the microbiome of stool samples from
64 treatment-naive MS patients and 68 healthy controls using
amplicon sequencing of the 16S V4 region of the rRNA gene. We
characterized immune profiles of cultured PBMC in response to
specific bacteria harbored by MS patients.
Results: We found that MS patients exhibited impaired in-vitro
Treg differentiation in response to their own microbiota. No major
shifts in microbial community structure were observed. However,
we were able to identify individual microbial taxa that were significantly
associated with MS and studied their ability to regulate
primary human T lymphocyte differentiation in vitro.
We next conducted in-vitro assays to characterize the functional
properties of the MS gut microbiota. We found that MS-associated
Acinetobacter calcoaceticus was sufficient to reduce Treg
differentiation and increase both Th1 and Th2 differentiation. The
expansion of Th1 lymphocytes was recapitulated by Akkermansia
muciniphila, which was also more abundant in MS patients.
In contrast, Parabacteroidesdistasonis, which was significantly
reduced in MS microbiomes, stimulated CD4+ T lymphocyte
differentiation into a CD25+ IL-10+ regulatory phenotype. Our
results suggest that MS-associated changes in microbiota alter
T lymphocyte differentiation in a complex fashion and likely
through multiple mechanisms.
Finally, microbiota transplants from MS patients into germ-free
mice results in more severe experimental autoimmune encephalomyelitis
and reduced Tregs compared to controls.
Conclusion: This study identifies specific human gut bacteria that
regulate adaptive autoimmune responses, suggesting therapeutic
targeting of the microbiota as a novel treatment for MS.

The MS-Associated Gut Microbiome

Provided is an isolated B. fragilis bacterial cell producing a native capsular polysaccharide A (PSA), wherein the cell is incapable of producing capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH because the cell's biosynthetic genes for native capsular polysaccharides PSB, PSC, PSD, PSE, PSF, PSG, and PSH have been deleted from the cell's genome. The isolated or wild type B. fragilis cell, or an extract obtained from said B. fragilis cell, can be used to treat individuals with inflammation.

Sarkis K. Mazmanian

Papers

Winning the Microbial Battle, but Not the War

Integrated multi-cohort analysis of the Parkinson’s disease gut metagenome

Commensal bacteria induce a barrier protective response to prevent sensitization to food allergens

The MS-Associated Gut Microbiome

Generation of Bacteriodes fragilis capsular polysaccharide A-only producing mutant strain