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)

The link between the microbes in the human gut and the development of obesity, cardiovascular disease and metabolic syndromes, such as type 2 diabetes, is becoming clearer. However, because of the complexity of the microbial community, the functional connections are less well understood. Studies in both mice and humans are helping to show what effect the gut microbiota has on host metabolism by improving energy yield from food and modulating dietary or the host-derived compounds that alter host metabolic pathways. Through increased knowledge of the mechanisms involved in the interactions between the microbiota and its host, we will be in a better position to develop treatments for metabolic disease.

Functional interactions between the gut microbiota and host metabolism

Recent years have witnessed the rise of the gut microbiota as a major topic of research interest in biology. Studies are revealing how variations and changes in the composition of the gut microbiota influence normal physiology and contribute to diseases ranging from inflammation to obesity. Accumulating data now indicate that the gut microbiota also communicates with the CNS — possibly through neural, endocrine and immune pathways — and thereby influences brain function and behaviour. Studies in germ-free animals and in animals exposed to pathogenic bacterial infections, probiotic bacteria or antibiotic drugs suggest a role for the gut microbiota in the regulation of anxiety, mood, cognition and pain. Thus, the emerging concept of a microbiota-gut-brain axis suggests that modulation of the gut microbiota may be a tractable strategy for developing novel therapeutics for complex CNS disorders.

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Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour

There is increasing, but largely indirect, evidence pointing to an effect of commensal gut microbiota on the central nervous system (CNS). However, it is unknown whether lactic acid bacteria such as Lactobacillus rhamnosus could have a direct effect on neurotransmitter receptors in the CNS in normal, healthy animals. GABA is the main CNS inhibitory neurotransmitter and is significantly involved in regulating many physiological and psychological processes. Alterations in central GABA receptor expression are implicated in the pathogenesis of anxiety and depression, which are highly comorbid with functional bowel disorders. In this work, we show that chronic treatment with L. rhamnosus (JB-1) induced region-dependent alterations in GABAB1b mRNA in the brain with increases in cortical regions (cingulate and prelimbic) and concomitant reductions in expression in the hippocampus, amygdala, and locus coeruleus, in comparison with control-fed mice. In addition, L. rhamnosus (JB-1) reduced GABAAα2 mRNA expression in the prefrontal cortex and amygdala, but increased GABAAα2 in the hippocampus. Importantly, L. rhamnosus (JB-1) reduced stress-induced corticosterone and anxiety- and depression-related behavior. Moreover, the neurochemical and behavioral effects were not found in vagotomized mice, identifying the vagus as a major modulatory constitutive communication pathway between the bacteria exposed to the gut and the brain. Together, these findings highlight the important role of bacteria in the bidirectional communication of the gut–brain axis and suggest that certain organisms may prove to be useful therapeutic adjuncts in stress-related disorders such as anxiety and depression.

https://www.pnas.org/content/pnas/108/38/16050.full.pdf

Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve.

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

/pdf/fast-tree-computing-large-minimum-evolution-trees-with-4grq0gwfpy.pdf

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Publisher Summary This chapter describes the methods for studying the adhesion of microorganisms to intestinal mucus, intestinal tissue culture cells, and intestinal mucosal tissue pieces. Although intestinal mucus and tissue culture cells provide convenient models for different parts of the mucosa, whole intestinal tissue probably provides the most realistic substratum for the study of adhesion to the intestinal mucosa. Tissue pieces can also be obtained from different parts of the intestine, which allows for studying possible site specific adhesion. In the case of tissue from human origin, it will usually be diseased tissue, though some healthy tissue is often resected together with this. Thus, the effect of different diseases on adhesion can be studied as well. Moreover, the effect of the normal microbiota present on the intestinal mucosa can be taken into account as well. A potential disadvantage with the use of tissue pieces, especially from human origin, may be the restricted availability and the requirement of immediate processing when available. The chapter also discusses how to determine the affinity of microorganisms for substrata and the maximum number of binding sites available on a substratum.

Microbial interactions to intestinal mucosal models.

Forty strains of enterococci and forty strains of lactobacilli isolated from feces of 10 healthy dogs were tested for the antimicrobial activity, tolerance to bile and adhesion activity. The total count of fecal enterococci reached 5.5 log CFU/g and of lactobacilli 7.6 log CFU/g. Screening for production of bacteriocin-like substances showed an to partly inhibit the growth ofEnterobacter sp. (hazy zones of inhibition). Ten strains ofEnterococcus sp. and nine strains ofLactobacillus sp. were found without any inhibitory activity against all indicators used. Seven enterococcal strains and six lactobacilli with the broadest antimicrobial spectrum were selected for further probiotic assays. In the presence of 1 % bile, the survival rate of selected enterococci (71.7–97.5 %) was higher than that of lactobacilli (66.7–75.4 %). The adhesion of strains to human intestinal mucus (5.1–8.2 % by enterococci, 2.7–8.3 % by lactobacilli) was found to be similar as adhesion to canine intestinal mucus (3.7–10.6 % by enterococci, 2.1–6.0 % by lactobacilli). Strain AD1, one lactobacillus isolate, reduced the higher level of serum cholesterol and alanine aminotransferase after oral administration to dogs suffering from diseases of the gastrointestinal tract.

Lactobacilli and enterococci--potential probiotics for dogs.

The effects of Lactobacillus acidophilus NCFM™, lactitol, and the combination of lactitol and L. acidophilus NCFM™ were studied with a semi-continuous colon fermentation simulation; consisting of compartments mimicking, ascending, transverse, descending and sigmoid colon and their conditions with faecal inoculation. L. acidophilus NCFM™ was detected throughout the colon simulator. Lactitol was utilised early on by the microbes in the proximal part of the simulator. Lactitol increased the total numbers of microbes and bifidobacteria, and decreased clostridia cluster IV, while L. acidophilus NCFM™ alone decreased the numbers of clostridia cluster XIV. Combination treatment increased the numbers of bifidobacteria. Furthermore, concentrations of acetic acid, butyric acid and the sum of total short-chain fatty acids were increased by both lactitol-including treatments. The treatment with L. acidophilus NCFM™ alone increased the concentration of propionic acid and butyric acid. L. acidophilus NCFM™ tended to in...

Arthur C. Ouwehand

Papers

Microbial interactions to intestinal mucosal models.

Lactobacilli and enterococci--potential probiotics for dogs.

Synbiotic effects of lactitol and Lactobacillus acidophilus NCFM™ in a semi-continuous colon fermentation model

Global analysis of clinical trials with probiotics.

Certain dietary carbohydrates promote Listeria infection in a guinea pig model, while others prevent it