Burkhardt Flemer

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.

Tumour-associated and non-tumour-associated microbiota in colorectal cancer

Objective A signature that unifies the colorectal cancer (CRC) microbiota across multiple studies has not been identified. In addition to methodological variance, heterogeneity may be caused by both microbial and host response differences, which was addressed in this study. Design We prospectively studied the colonic microbiota and the expression of specific host response genes using faecal and mucosal samples (‘ON’ and ‘OFF’ the tumour, proximal and distal) from 59 patients undergoing surgery for CRC, 21 individuals with polyps and 56 healthy controls. Microbiota composition was determined by 16S rRNA amplicon sequencing; expression of host genes involved in CRC progression and immune response was quantified by real-time quantitative PCR. Results The microbiota of patients with CRC differed from that of controls, but alterations were not restricted to the cancerous tissue. Differences between distal and proximal cancers were detected and faecal microbiota only partially reflected mucosal microbiota in CRC. Patients with CRC can be stratified based on higher level structures of mucosal-associated bacterial co-abundance groups (CAGs) that resemble the previously formulated concept of enterotypes. Of these, Bacteroidetes Cluster 1 and Firmicutes Cluster 1 were in decreased abundance in CRC mucosa, whereas Bacteroidetes Cluster 2, Firmicutes Cluster 2, Pathogen Cluster and Prevotella Cluster showed increased abundance in CRC mucosa. CRC-associated CAGs were differentially correlated with the expression of host immunoinflammatory response genes. Conclusions CRC-associated microbiota profiles differ from those in healthy subjects and are linked with distinct mucosal gene-expression profiles. Compositional alterations in the microbiota are not restricted to cancerous tissue and differ between distal and proximal cancers.

Diversity and antimicrobial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp.

Aims:  To evaluate the diversity and antimicrobial activity of bacteria from the marine sponges Suberites carnosus and Leucosolenia sp.

Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges

The microbiota of four individual deep water sponges, Lissodendoryx diversichela, Poecillastra compressa, Inflatella pellicula, and Stelletta normani, together with surrounding seawater were analysed by pyrosequencing of a region of the 16S rRNA gene common to Bacteria and Archaea. Due to sampling constraints at depths below 700 m duplicate samples were not collected. The microbial communities of L. diversichela, P. compressa and I. pellicula were typical of low microbial abundance (LMA) sponges while S. normani had a community more typical of high microbial abundance (HMA) sponges. Analysis of the deep sea sponge microbiota revealed that the three LMA-like sponges shared a set of abundant OTUs that were distinct from those associated with sponges from shallow waters. Comparison of the pyrosequencing data with that from shallow water sponges revealed that the microbial communities of all sponges analysed have similar archaeal populations but that the bacterial populations of the deep sea sponges were distinct. Further analysis of the common and abundant OTUs from the three LMA-like sponges placed them within the groups of ammonia oxidising Archaea (Thaumarchaeota) and sulphur oxidising γ-Proteobacteria (Chromatiales). Reads from these two groups made up over 70% of all 16S rRNA genes detected from the three LMA-like sponge samples, providing evidence of a putative common microbial assemblage associated with deep sea LMA sponges.

Archaea Appear to Dominate the Microbiome of Inflatella pellicula Deep Sea Sponges

Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising ∼60% and ∼72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (∼11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising ∼88% and ∼89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (∼0.2% and ∼0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.

Marine Sponges – Molecular Biology and Biotechnology

Marine sponges are an ancient and diverse animal phylum that host well-established symbiotic microbial communities. The vast majority of the microbial genetic diversity in sponges is, however, currently inaccessible by traditional methods. This large genetic resource may be of use for biotechnological applications, particularly as the physicochemical parameters under which the genes within these microbes function are likely to dictate that they may be significantly different from similar genes or gene products currently in use in industry, offering in some instances improved performance. Emerging tools and technologies in the field of metagenomics offer enormous potential for the discovery and exploitation of new biosynthetic entities. Both sequence-based and function-based technologies have to date been employed to identify genes with novel or improved functions. Marine sponges, as well-recognized sources of novel marine natural products with varied applications, are the ideal target for the implementation of these new technologies. We detail here some successes in the discovery and development of marine natural products for industrial or pharmaceutical applications and we also highlight some technical impediments to gene and gene product exploitation which as yet still need to be overcome.

From Culture to High-Throughput Sequencing and Beyond: A Layperson’s Guide to the “Omics” and Diagnostic Potential of the Microbiome

Detailed knowledge of the community of organisms in the gut has become possible in recent years because of the development of culture-independent methods. Largely based on latest DNA sequencing platforms, it is now possible to establish the composition of the microbiota and the repertoire of biochemical functions it encodes. Variations in either or both of these parameters have been linked to intestinal and extraintestinal disease. This article summarizes how these methods are applied, with special reference to gastroenterology, and describes the achievements and future potential of microbiota analysis as a diagnostic tool.

Studying the Microbiome: "Omics" Made Accessible.

The term microbiome refers to the collection of microbes or microbial genes in a specified location or clinical sample. Identifying micro-organisms has historically relied upon bacteriological culture, which is time consuming and difficult to effectively implement. The recent adaptation of culture-independent techniques for profiling microbial communities, allied with next-generation massively parallel DNA sequencing, allows clinician scientists to determine the entire microbial content of a specimen to a forensic level of detail within 48 hours. The technology is still young, and the main thrust of current efforts is to identify how changes in the microbiome covary with a variety of syndromes and diseases, and to determine if these changes are causative or consequential. Regardless of the outcome of these investigations, it is already apparent that the gut microbiome is a useful biomarker for intestinal and extraintestinal disease. In this review, the authors summarize the main concepts in microbiome analysis, and prospects for the microbiomes clinical deployment.

Evidence of a putative deep sea specific microbiome in marine sponges (PLoS ONE (2014) 9, 3 (e91092) DOI:10.1371/journal.pone.0091092)

Citation: The PLOS ONE Staff (2014) Correction: Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges. PLoS ONE 9(7): e103400. doi:10.1371/ journal.pone.0103400 Published July 18, 2014 Copyright: 2014 The PLOS ONE Staff. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.