Coral reefs are the most biodiverse of all marine ecosystems; however, very little is known about prokaryotic diversity in these systems. To address this issue, we sequenced over 1000 bacterial 16S rDNAs from 3 massive coral species (Montastraea franksi, Diploria strigosa, and Porites astreoides) in Panama and Bermuda. Analysis of only 14 coral samples yielded 430 distinct bacterial ribotypes. Statistical analyses suggest that additional sequencing would have resulted in a total of 6000 bacterial ribotypes. Half of the sequences shared < 93% identity to previously published 16S sequences, and therefore probably represent novel bacterial genera and species; this degree of novelty was substantially higher than that observed for other marine samples. Samples from the Panama corals were more diverse than those from Bermuda, paralleling diversity gradients seen in metazoans. The coral-bacteria associations were non-random. Different coral species had distinct bacterial communities, even when physically adjacent, while bacterial communities from the same coral species separated by time (~1 yr) or space (3000 km) were similar. Analysis of the branching coral Porites furcata showed that bacterial ribotypes can also be structured spatially within colonies. Therefore, corals and reefs represent landscapes of diverse, ecologically structured prokaryotic communities. KEY WORDS: Coral · Bacteria · 16S rDNA · Biodiversity Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 243: [1][2][3][4][5][6][7][8][9][10] 2002 1973, Mitchell & Chet 1975, Ducklow & Mitchell 1979, Pascal & Vacelet 1981, Segel & Ducklow 1982, Herndl & Velimirov 1986, Paul et al. 1986, Williams et al. 1987, Shashar et al. 1994, Ritchie & Smith 1995, 1997, Santavy 1995, Kushmaro et al. 1996, Santavy & Peters 1997, Frias-Lopez et al. 2002. Whether these communities are just passive associations with water column bacteria or if they are specific associations with ecological importance is in dispute. Ritchie & Smith (1997) used carbon source utilization patterns of bacteria cultured from the mucus layer (aka: mucopolysaccharide layer, MPSL; coral surface microlayer, CMS) to demonstrate that Caribbean coral species had unique, species-specific mucus-associated microbial communities. Rohwer et al. (2001) built upon this work and used a 16S rDNA culture-independent method (PCR and denaturing gradient gel electrophoresis, DGGE) to demonstrate that Montastraea franksi had a diverse bacterial community that was similar in 25 samples from 5 reefs, up to 10 km apart. Comparison of coralassociated and overlaying water column bacterial communities in this study showed that there is almost no overlap . Similarly, Frias-Lopez et al. (2002) and Durkin et al. (unpubl.) found the bacteria in overlaying water were not the same as those associated with corals. Santavy (1995) observed that Porites astreoides harbors a bacterial species, possibly Moraxella sp., that forms ovoids within P. astreoides and seems to participate ...

SUMMARY The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, 72 of which had mild/moderate (stage 0–2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis). We identified a set of forty features (p-value <0.006), which included 37 bacterial species that were used to construct a Random Forest classifier model to distinguish mild/moderate NAFLD from advanced fibrosis. The model had a robust diagnostic accuracy (AUC 0.936) for detecting advanced fibrosis. This study provides preliminary evidence for a novel fecal-microbiome derived metagenomic signature to detect advanced fibrosis in NAFLD.

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human fecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and totals 1.68% of all human fecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologs and a unique carbohydrate-binding domain encoded in the phage genome,.

Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples. microbiome | genomics | sequencing

Viruses are ubiquitous components of the marine environment, frequently reaching concentrations of 107–108 viruses per milliliter of surface seawater. The majority of these viral particles are bacteriophages (phages). Although the oceans are probably the largest pool of bacteriophages on the planet, the evolutionary relationships of marine phages to phages from other environments are unknown. To address this issue, we have completely sequenced the genome of the lytic marine phage, Roseophage SIO1, that infects the heterotrophic marine bacterium Roseobacter SIO67. This phage has an isometric capsid with a diameter of approximately 43 nm, a short tail, a buoyant density of 1.49 g cm‐3 in CsCl, and a 39,906‐bp dsDNA genome. Sequence similarities and relative positions within the genome suggest that three of the open reading frames (ORFs) are homologous to the primase, DNA polymerase, and endodeoxyribonuclease I proteins of coliphages T3 and T7. The results are consistent with the mosaic theory of phage evolution and indicate a genetic link between marine and nonmarine phages. Additionally, basic life histories of marine phages can be elucidated by comparison of complete genomes to those of other extensively studied phages (e.g., lambda, T4, T7). The DNA replication machinery of Roseophage SIO1 shows a clear homology with that of coliphages T3 and T7, suggesting that the process of DNA replication may be similar among these phages. The Roseophage SIO1 genome also encodes four predicted proteins involved in phosphate metabolism (RP PhoH, RP ribonucleotide reductase, RP Thy1, and RP endodeoxyribonuclease I) suggesting that phosphate recycling is important to Roseophage SIO1's life cycle. Other interesting clues about Roseophage SIO's life history come from the absence of certain expected protein regions. For example, we have not been able to identify the Roseophage SIO1 structural proteins (e.g., capsid proteins) by homology to other phages. It is also conspicuous that the Roseo‐phage SIO1 genome lacks a recognizable RNA polymerase, an essential component of T3 and T7 life cycles. Analysis of the Roseophage SIO1 genome shows that marine and nonmarine phages are genetically related but basic life histories may be significantly different.