Reconstruction of ancient microbial genomes from the human gut.

Loss of gut microbial diversity1-6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000-2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

Transcriptomics and physiological analyses reveal co-ordinated alteration of metabolic pathways in Jatropha curcas drought tolerance.

Jatropha curcas, a multipurpose plant attracting a great deal of attention due to its high oil content and quality for biofuel, is recognized as a drought-tolerant species. However, this drought tolerance is still poorly characterized. This study aims to contribute to uncover the molecular background of this tolerance, using a combined approach of transcriptional profiling and morphophysiological characterization during a period of water-withholding (49 d) followed by rewatering (7 d). Morphophysiological measurements showed that J. curcas plants present different adaptation strategies to withstand moderate and severe drought. Therefore, RNA sequencing was performed for samples collected under moderate and severe stress followed by rewatering, for both roots and leaves. Jatropha curcas transcriptomic analysis revealed shoot- and root-specific adaptations across all investigated conditions, except under severe stress, when the dramatic transcriptomic reorganization at the root and shoot level surpassed organ specificity. These changes in gene expression were clearly shown by the down-regulation of genes involved in growth and water uptake, and up-regulation of genes related to osmotic adjustments and cellular homeostasis. However, organ-specific gene variations were also detected, such as strong up-regulation of abscisic acid synthesis in roots under moderate stress and of chlorophyll metabolism in leaves under severe stress. Functional validation further corroborated the differential expression of genes coding for enzymes involved in chlorophyll metabolism, which correlates with the metabolite content of this pathway.

A Peek into the Plasmidome of Global Sewage.

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here, we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105-Gbp Oxford Nanopore and 167-Gbp Illumina NextSeq DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 carried genes encoding for plasmid-related and 11,222 for virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids. Those that exhibited similarity had similarity to plasmids whose hosts were previously detected in these sewage samples (e.g., Acinetobacter, Escherichia, Moraxella, Enterobacter, Bacteroides, and Klebsiella). Some AMR classes were detected at a higher abundance in plasmidomes (e.g., macrolide-lincosamide-streptogramin B, macrolide, and quinolone) compared to the respective complex sewage samples. In addition to AMR genes, a range of functions were encoded on the candidate plasmids, including plasmid replication and maintenance, mobilization, and conjugation. In summary, we describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes. Moreover, the obtained data could provide further valuable insight into the ecology and evolution of microbiomes, knowledge about AMR transmission, and the discovery of novel functions. IMPORTANCE This is, to the best of our knowledge, the first study to investigate plasmidomes at a global scale using long read sequencing from complex untreated domestic sewage. Previous metagenomic surveys have detected AMR genes in a variety of environments, including sewage. However, it is unknown whether the AMR genes were present on the microbial chromosome or located on extrachromosomal elements, such as plasmids. Using our approach, we recovered a large number of plasmids, of which most appear novel. We identified distinct AMR genes that were preferentially located on plasmids, potentially contributing to their transmissibility. Overall, plasmids are of great importance for the biology of microorganisms in their natural environments (free-living and host-associated), as well as for molecular biology and biotechnology. Plasmidome collections may therefore be valuable resources for the discovery of fundamental biological mechanisms and novel functions useful in a variety of contexts.

Draft Genome Sequence of Andreprevotia sp. Strain IGB-42, a Chitinolytic Bacterium Isolated from a Soil Sample of an Anthill in Stuttgart, Germany.

Andreprevotia sp. strain IGB-42 is a chitin-degrading bacterium isolated from the soil of an anthill. The genome contains 4.7 Mb, a G+C content of 61.31%, 4,257 predicted open reading frames, and a set of industrially interesting chitinase genes.

Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance.

One Health surveillance of antimicrobial resistance (AMR) depends on a harmonized method for detection of AMR. Metagenomics-based surveillance offers the possibility to compare resistomes within and between different target populations. Its potential to be embedded into policy in the future calls for a timely and integrated knowledge dissemination strategy. We developed a blended training (e-learning and a workshop) on the use of metagenomics in surveillance of pathogens and AMR. The objectives were to highlight the potential of metagenomics in the context of integrated surveillance, to demonstrate its applicability through hands-on training and to raise awareness to bias factors. The target participants included staff of competent authorities responsible for AMR monitoring and academic staff. The training was organized in modules covering the workflow, requirements, benefits and challenges of surveillance by metagenomics. The training had 41 participants. The face-to-face workshop was essential to understand the expectations of the participants about the transition to metagenomics-based surveillance. After revision of the e-learning, we released it as a Massive Open Online Course (MOOC), now available at https://www.coursera.org/learn/metagenomics. This course has run in more than 20 sessions, with more than 3,000 learners enrolled, from more than 120 countries. Blended learning and MOOCs are useful tools to deliver knowledge globally and across disciplines. The released MOOC can be a reference knowledge source for international players in the application of metagenomics in surveillance.

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.

Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: (i) human hosts, (ii) ambiguousness/contaminants in public microbial reference genomes and (iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism that was determined in cultivation- and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management.

The Molecular Blueprint of a Fungus by Next-Generation Sequencing (NGS).

Sequencing the whole genome of an organism is invaluable for its comprehensive molecular characterization and has been drastically facilitated by the advent of high-throughput sequencing techniques. Especially in clinical microbiology the impact of sequenced strains increases as resistance and virulence markers can easily be detected. Here, we describe a combined approach for sequencing a fungal genome and transcriptome from initial nucleic acid isolation through the generation of ready-to-load DNA libraries for the Illumina platform and the final step of genome assembly with subsequent gene annotation.

Draft Genome Sequence of Pseudonocardia autotrophica Strain DSM 43083, an Efficient Producer of Peroxidases for Lignin Modification.

Pseudonocardia autotrophica strain DSM 43083 is a filamentous actinobacterium and was described to degrade or modify lignin. Here, we present its draft genome sequence, with a size of 5.8 Mb, to unravel the gene set coding for promising monooxygenases, dioxygenases, and DyP-type peroxidases associated with aromatic metabolism and lignin modification.

Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes.

The three Actinobacteria strains Streptomyces platensis DSM 40041, Pseudonocardia autotrophica DSM 535, and Streptomyces fradiae DSM 40063 were described to selectively oxyfunctionalize several drugs. Here, we present their draft genomes to unravel their gene sets encoding promising cytochrome P450 monooxygenases associated with the generation of drug metabolites.

Draft Genome Sequence of Amantichitinum ursilacus IGB-41, a New Chitin-Degrading Bacterium.

Amantichitinum ursilacus IGB-41 is a new species of chitin-degrading bacterium isolated from soil, which secretes potential industrial enzymes. The genome of A. ursilacus was sequenced, and the gene set encoding chitinases was identified. Here, we present the draft genome of 4.9 Mb, comprising 38 contigs, and the corresponding annotation.