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The excavation of the Merovingian cemetery of Saint-Linaire (France) was an opportunity to describe the completeness of the tombs preserved from soil erosion. An anthropobiological study was carried out on the osteological material and the different categories of graves. On the basis of a complete archaeo-anthropological corpus we have undertaken an analysis of the differential preservation of the bones according to the different archaeobiological parameters such as the type of bone, the individual age but also the type of grave such as earthen graves, coffin, or sarcophagus. In order to establish whether and how funerary practices had impacted the early diagenesis of the bones, FTIR was used to investigate the carbonate and fluoride content of the bones, and the infra-red splitting factor (SF), while XRD analysis was performed to estimate the crystallinity index (CI). In addition, the micro, macro and total porosity of the bones were measured by water adsorption, and bone carbon and nitrogen amounts were obtained by EA IRMS. These diagenetic variables were analysed with regards to environmental (grave filling: humus, calcareous, clay), cultural (type of grave) and biological (mature versus immature individuals) factors. While there is a tendency of a better preservation of the skeletons in humus, and of juvenile bones to show less post-mortem alteration than the adult skeletons, the most important factor which determines the fate of the skeleton is the type of bone, with a preferential preservation of the ribs at Saint-Linaire.

Trilobites are the most diverse animal phylum in the Cambrian, and are critical stratigraphic markers. Despite their significance, the exact sequence of trilobite appearances across the globe, and their respective ages, are difficult to reconstruct due to a scarcity of radiometric dates. Using visual correlation of carbon isotope (δ13C) excursions and integration of available U-Pb age constraints, Landing et al. (2021) have estimated the age of the first Siberian trilobites at roughly 521 million years ago (Ma), which would make them the world’s oldest trilobites. Here, we aim to provide a more precise date, with uncertainty, using a Bayesian stratigraphic age model that takes the global signature of δ13C excursions to correlate proxy records from multiple locations. Our model integrates radiometric dates across sections, using ages from well-dated sections to inform age estimates in sections with little or no age information. The model works by evaluating the fit of Bayesian splines to different alignments of the sections, using Markov chain Monte Carlo methods to obtain the posterior distributions. This approach provides an objective evaluation of different possible alignments, generating a probabilistic age-depth model. We apply this model to the lower Cambrian sections of the Anti-Atlas mountains in Morocco, and to the Sukharikha River section of the northwestern Siberian platform. The Moroccan sections provide a uniquely detailed δ13C record and multiple radiometric dates, and this age information is transferred to the Siberian section and the emergence of trilobites in the fossil record. Preliminary results indicate that the first appearance of Siberian trilobites is younger than previously estimated, and consequently closer in time to the first trilobites in Morocco and elsewhere.Landing, E., Schmitz, M., Geyer, G., Trayler, R., & Bowring, S. (2021). Precise early Cambrian U–Pb zircon dates bracket the oldest trilobites and archaeocyaths in Moroccan West Gondwana. Geological Magazine, 158(2), 219-238.

Background The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research. Methods Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool’s output. Results VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception. Conclusions This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools.

This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

Peroxynitrite is a reactive intermediate formed in vivo through uncatalysed reaction of superoxide and nitric oxide radicals. Despite significant interest in detecting peroxynitrite in vivo and understanding its production, little attention has been given to the evolutionary origins of peroxynitrite signalling. Herein we focus on two enzymes that are key to the biosynthesis of superoxide and nitric oxide, NADPH oxidase 5 (NOX5) and endothelial nitric oxide synthase (eNOS), respectively. Multiple sequence alignments of both enzymes including homologues from all domains of life, coupled with a phylogenetic analysis of NOX5, suggest eNOS and NOX5 are present in animals as the result of horizontal gene transfer from ancestral cyanobacteria to ancestral eukaryotes. Therefore, biochemical studies from other laboratories on a NOX5 homologue in Cylindrospermum stagnale and an eNOS homologue in Synechococcus sp. PCC 7335 are likely to be of relevance to human NOX5 and eNOS and to the production of superoxide, nitric oxide and peroxynitrite in humans.

RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO2 and O2. To compensate, organisms have evolved convergent solutions to concentrate CO2 around the active site. The genetic engineering of such inorganic carbon concentrating mechanisms (CCMs) into plants could help facilitate future global food security for humankind. In bacteria, the carboxysome represents one such CCM component, of which two independent forms exist: α and β. Cyanobacteria are important players in the planet’s carbon cycle and the vast majority of the phylum possess a β-carboxysome, including most cyanobacteria used as laboratory models. The exceptions are the exclusively marine Prochlorococcus and Synechococcus that numerically dominate open ocean systems. However, the reason why marine systems favor an α-form is currently unknown. Here, we report the genomes of 58 cyanobacteria, closely related to marine Synechococcus that were isolated from freshwater lakes across the globe. We find all these isolates possess α-carboxysomes accompanied by a form 1A RuBisCO. Moreover, we demonstrate α-cyanobacteria dominate freshwater lakes worldwide. Hence, the paradigm of a separation in carboxysome type across the salinity divide does not hold true, and instead the α-form dominates all aquatic systems. We thus question the relevance of β-cyanobacteria as models for aquatic systems at large and pose a hypothesis for the reason for the success of the α-form in nature.

Extensively drug-resistant Acinetobacter baumannii (XDR-AB) is a major threat to public health worldwide. A retrospective study for 27 XDR-AB isolates from four tertiary hospitals in Thailand was c...

This study reports the first dietary stable isotope data from Iron Age in Latvia. Archaeological, osteological, genetic, and stable isotope data from the Lejasbitēni cemetery were used to study gendered differences in childhood diet expressed in stable isotope ratios with social status expressed in grave goods, in this population from the 7th – 10th centuries CE. Carbon and nitrogen isotope analysis showed significant differences in childhood diet between male and female gendered individuals, indicating that gender might have been a key factor for dietary differences in children. There were no significant dietary differences within the gender groups in adults of differential social status expressed in grave goods, suggesting no link between childhood diet and social status in adulthood, although the sample size was very small. A change towards a more hierarchical society was observed in the later period of the cemetery, expressed in the appearance of more elaborately furnished burials, rare grave goods, and a new burial tradition. All these changes were contemporary with the development of the Viking Age in Northern Europe, and thus possibly signified external cultural influence. Ancient DNA analysis showed that gender as expressed by grave goods corresponded with biological sex in two individuals with the highest quality aDNA, while biological sex could not be confirmed in the other five tested individuals.

Bacteriophages are as ubiquitous as their bacterial hosts and often more abundant. Understanding how bacteriophages control their bacterial host populations requires a number of different approaches. Bacteriophages can control bacterial populations through lysis, drive evolution of bacterial immunity systems through infection, provide a conduit for horizontal gene transfer and alter host metabolism by carriage of auxiliary metabolic genes. Understanding and quantifying how bacteriophages drive these processes, requires both technological developments to take measurements in situ, and laboratory-based studies to understand mechanisms. Technological advances have allowed quantification of the number of infected cells in situ, revealing far-lower levels than expected. Understanding how observations in laboratory conditions relate to what occurs in the environment, and experimental confirmation of the predicted function of phage genes from observations in environmental omics data, remains challenging.

Colonial New Zealand was built on the ideal of creating better lives for settlers. Emigrants came looking to escape the shackles of the class-system and poor conditions in Industrial Revolution period Britain. Colonial propaganda claimed that most emigrants achieved their aims, but the lives the colonists actually experienced upon reaching New Zealand remain relatively unexplored from a biosocial perspective. In this paper we present a pilot study of stable isotope results of bone collagen from seven adults interred in the St. John’s Cemetery (SJM), Milton, New Zealand (ca. AD 1860–1900). We interpret the diet at Milton and broadly compare our isotopic results with contemporaneous samples from Britain. We show that, like contemporary Britain, the diet of our studied individuals was focused on C3 crops and terrestrial meat sources. Despite higher ????15N values in contemporary UK populations (which can simplistically be interpreted as indicative of higher meat intake), consideration of different local baselines makes it likely that this New Zealand population had relatively similar levels of meat intake. Interestingly marine resources did not form an important part of the Milton diet, despite the site's proximity to the ocean, hinting at the possible stigmatisation of local resources and the development of a European New Zealand (pākehā) food identity.

The bacteriophage vB_AhM_PVN02 (PVN02), infecting Aeromonas hydrophila, was isolated from a striped catfish pond water sample in Can Tho City, Vietnam. The phage had high lytic activity with a latent period and burst size of approximately 20 min and 105 plaque-forming units per cell, respectively. Observation of the phage by transmission electron microscopy indicated that PVN02 belongs to the family Myoviridae. The genome of PVN02 is a double-stranded linear DNA with a length in 51,668 bp and a content of 52% GC. Among the 64 genes, 16 were predicted to encode proteins with predicted functions. No virulence or antibiotic resistance genes were found in the genome, suggesting it would be a useful biocontrol agent. Classification of the phage based on sequence comparisons, phylogenetic analysis, and gene-sharing networks was carried out, and it was found to be the first representative of a new species within a previously undefined genus in the family Myoviridae. This study confirmed that PVN02 is a novel lytic phage that could potentially be used as an agent to control Aeromonas hydrophila in striped catfish in the Mekong Delta, Vietnam.

Aims This study describes the effect of phage therapy on hatching of longfin yellowtail (Seriola rivoliana) eggs challenged with Photobacterium damselae subsp. damselae. Methods and results A lytic phage (vB_Pd_PDCC-1) against P. damselae subsp. damselae was isolated and characterized. The use of phage vB_Pd_PDCC-1 increased the hatching rate of eggs, and reduced presumptive Vibrio species to non-detectable numbers, even in non-disinfected eggs. High-throughput 16S rRNA gene sequencing analysis revealed that phage vB_Pd_PDCC-1 caused significant changes in the composition and structure of the associated microbiota, allowing that members (e.g. those belonging to the family Vibrionaceae) of the class Gammaproteobacteria to be displaced by members of the class Alphaproteobacteria. Conclusions To the best of our knowledge, this represents the first study evaluating phage therapy to control potential negative effects of P. damselae subsp. damselae during hatching of longfin yellowtail eggs. Significance and impact of the study The Seriola genus includes several important commercial fish species due to its rapid growth and easy adaptability to confinement conditions. However, bacterial infections (especially those caused by Vibrio and Photobacterium species) are among the main limiting factors for the intensification of marine fish aquaculture, particularly during early development stages. Therefore, the use of phages, which are natural killers of bacteria, represents a promising strategy to reduce the mortality of farmed organisms caused by pathogenic bacteria.

Inhumation burials are recorded in Britain and Europe during excavations in a standardized way, especially graves of early medieval date. Just a limited number of attributes are usually foregrounded and these mainly concern skeletal identification, the grave plan and, when a burial is furnished, a list of objects, particularly metalwork, as well as occasional reference to burial structures, if present. In this paper, we argue that concealed within these recorded details are attributes that often receive little attention, but which can provide evidence for community investment in the individual funerary rite. These include grave orientation, grave morphology, the body position and the empty spaces in the grave, as well as categories of material culture. We argue here that these factors enable us to define communal burial profiles and can facilitate the identification of group perceptions and actions in dealing with death. By capitalizing on these additional aspects of funerary ritual, archaeologists can move away from a general dependency on well-furnished burials as the main stepping-off point for discussion of social and cultural issues. This has particular relevance for regions where unfurnished burial rites are the norm and where furnished rites do not rely on a wealth of metalwork.

Objectives: Colonial period New Zealand was lauded as a land of plenty, where colonists could improve their station in life and secure a future for their families. Our understanding of colonial experience, however, is often shaped by historical records which communicate a state‐sponsored version of history. This study aims to reconstruct the lives of settlers using isotopic evidence from the colonial skeletons themselves. Materials and methods: We use skeletal remains from recently excavated colonial sites in Otago (South Island, New Zealand) to illustrate the information that can be gleaned from the isotopic analysis of individuals. We use 87Sr/86Sr to identify European settlers, and δ13C and δ15N from collagen and hair keratin, as well as dental enamel carbonate δ13C to trace dietary change over their life‐courses. Results: Strontium isotope analysis shows that all adults in our sample are non‐local. Dietary isotopes show that while most individuals had relatively consistent childhood diet, one individual with more rural origins likely had seasonal use of resources during childhood. While some members of the population seem to have increased their meat intake in the new colony most do not have clear evidence for this. Discussion: We show the diversity of human experience in first‐generation New Zealanders both prior to emigration and in the new colony. Despite colonial propaganda claiming that circumstances in New Zealand were improved for all settlers, we have little evidence for this, aside from among individuals of potentially high status.

Nontyphoidal Salmonella spp. are a leading cause of human food poisoning and can be transmitted to humans via consuming contaminated pork. To reduce Salmonella spread to the human food chain, bacteriophage (phage) therapy could be used to reduce bacteria from animals' preslaughter. We aimed to determine if adding a two-phage cocktail to feed reduces Salmonella colonization in piglets. This first required spray drying phages to allow them to be added as a powder to feed, and phages were spray dried in different excipients to establish maximum recovery. Although laboratory phage yields were not maintained during scale up in a commercial spray dryer (titers fell from 3 × 108 to 2.4 × 106 PFU/g respectively), the phage titers were high enough to progress. Spray dried phages survived mixing and pelleting in a commercial feed mill, and sustained no further loss in titer when stored at 4°C or barn conditions over 6 months. Salmonella-challenged piglets that were prophylactically fed the phage-feed diet had significantly reduced Salmonella colonization in different gut compartments (P

Waste from dairy production is one of the world’s largest sources of contamination from antimicrobial resistant bacteria (ARB) and genes (ARGs). However, studies to date do not provide necessary evidence to inform antimicrobial resistance (AMR) countermeasures. We undertook a detailed, interdisciplinary, longitudinal analysis of dairy slurry waste. The slurry contained a population of ARB and ARGs, with resistances to current, historical and never-used on-farm antibiotics; resistances were associated with Gram-negative and Gram-positive bacteria and mobile elements (ISEcp1, Tn916, Tn21-family transposons). Modelling and experimental work suggested that these populations are in dynamic equilibrium, with microbial death balanced by fresh input. Consequently, storing slurry without further waste input for at least 60 days was predicted to reduce ARB spread onto land, with >99% reduction in cephalosporin resistant Escherichia coli. The model also indicated that for farms with low antibiotic use, further reductions are unlikely to reduce AMR further. We conclude that the slurry tank is a critical point for prevalence and control of AMR, and that measures to limit the spread of AMR from dairy waste should combine responsible antibiotic use, including low total quantity, avoidance of human critical antibiotics, and choosing antibiotics with shorter half-lives, coupled with appropriate slurry storage.

The aims of this study were to explore the origins of 19 children buried in two mass graves and the general cemetery at the post-medieval St Gertrude Church cemetery in Riga, Latvia, using strontium isotope analysis (87Sr/86Sr), and to establish local soil Sr biosphere ranges from faunal samples from two areas of Latvia. The results confirmed the presence of one clear outlier in the population and one child who may have had originated from the region of Vidzeme. The lack of significant differences in 87Sr/86Sr between the other individuals analysed suggested that they were representative of one population. A strong correlation between 87Sr/86Sr ratios and previously obtained mean δ13C and δ15N values in children from mass graves suggested possible short-term dietary changes with increased proportion of marine resources and food sources subject to sea spray. The study has yielded the first comparative 87Sr/86Sr data from archaeological skeletons in Latvia, which will be essential for future research addressing comparative mobility studies in the region.

Experiences of childhood in colonial New Zealand are difficult to reconstruct from the historical record alone. Many of those who came to the colony were illiterate, and the Victorian tendency to avoid discussion of pregnancy and breastfeeding practices restricts our understanding of this important period. Bioarchaeological investigation, however, has the potential to illuminate the life stories of these first-generation Pākehā (European) settlers. Here we use isotopic evidence combined with dental pathology from children interred in a historic cemetery from Otago, New Zealand, to examine colonial childhood. We show how weaning practices in the colony differ from those experienced by their emigrant parents, highlight periods of illness likely associated with the weaning process, and bring to light the potential problems caused by maternal Vitamin D deficiency in the colony.

Infections caused by multidrug resistant Salmonella strains are problematic in swine and are entering human food chains. Bacteriophages (phages) could be used to complement or replace antibiotics to reduce infection within swine. Here, we extensively characterised six broad host range lytic Salmonella phages, with the aim of developing a phage cocktail to prevent or treat infection. Intriguingly, the phages tested differed by one to five single nucleotide polymorphisms. However, there were clear phenotypic differences between them, especially in their heat and pH sensitivity. In vitro killing assays were conducted to determine the efficacy of phages alone and when combined, and three cocktails reduced bacterial numbers by ~2 × 103 CFU/mL within two hours. These cocktails were tested in larvae challenge studies, and prophylactic treatment with phage cocktail SPFM10-SPFM14 was the most efficient. Phage treatment improved larvae survival to 90% after 72 h versus 3% in the infected untreated group. In 65% of the phage-treated larvae, Salmonella counts were below the detection limit, whereas it was isolated from 100% of the infected, untreated larvae group. This study demonstrates that phages effectively reduce Salmonella colonisation in larvae, which supports their ability to similarly protect swine.

Megaphages, bacteriophages harbouring extremely large genomes, have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of megaphages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other megaphages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including a NADP-dependent isocitrate dehydrogenase [Idh] and nicotinamide-nucleotide amidohydrolase [PncC], which have not previously been identified in megaphages. Mar_Mega_1 was abundant in a marine virome sample and related phages are widely prevalent in the oceans.

Carbon and nitrogen isotope profiles were obtained from incremental dentine analysis of 19 non‐adults from a cemetery in Riga, Latvia. The research compared the life histories and diet between people buried in two mass graves and the general cemetery. The δ13C profiles of several children from the mass graves were similar but did not resemble the patterns seen in children from the general cemetery, suggesting that they probably represented a different population group. The rise in δ15N values towards the end of the life of four individuals from one mass grave suggests they were victims of an historically documented famine.

The Asia-Pacific region is vast, with diverse cultures and political systems, yet all countries are connected by the common resource, the seas. Through limited, shallow regionalization, and globalization in general, the sea links are becoming stronger and the exploitation of the seas is rising, forcing the sovereign states to cooperate in even more fields, from transport, to natural disaster early warning systems, to security, to fisheries. Whilst these individual areas are seeing a growth in cooperation agreements, the ASEAN region has yet to follow the European Union in establishing an integrated maritime policy that brings all industries that use the seas and oceans under one umbrella. The EU’s integrated policy encompasses transport, energy, fishing, tourism, and trade with a view to forging the sustainable use of the seas. This paper looks at the main reasons why ASEAN and its plus members are unlikely to establish an integrated maritime policy, namely the various territorial disputes across the region and the unwillingness to cede sovereignty that such an integrated policy demands. As such, this paper assumes that an integrated maritime policy in Asia is required, but alas is infeasible with the ASEAN Way.

Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its’ potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation., Measurement(s)genome • sequence_assemblyTechnology Type(s)DNA sequencing • genome assemblySample Characteristic - OrganismSphingomonas paucimobilisSample Characteristic - Environmentoil contaminated soilSample Characteristic - LocationMalaysia Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9971711

Objectives: To identify and characterize anthropogenic lead sources on a 17th/18th century Barbadian plantation and to test if lead isotope analyses can be used to identify the geographic origins of first‐generation African captives. Materials and Methods: We carried out lead (Pb) isotope analyses on dental enamel samples from 24 individuals from the Newton Plantation Cemetery in Barbados, which had previously been analyzed for strontium (Sr) and oxygen (O) isotope composition (Schroeder et al., American Journal of Physical Anthropology, 2009, 139:547–557) and Pb concentrations (Schroeder et al., American Journal of Physical Anthropology, 2013, 150:203–209. Results: We are able to identify British Pb sources, and more specifically Bristol/Mendips Pb, as the most likely source of anthropogenic Pb on the plantation, highlighting the impact of the British Atlantic economy on the lives of enslaved peoples in Barbados during the period of plantation slavery. Furthermore, we find that there is only one clear outlier among seven individuals who had previously been identified as African‐born based on their enamel Sr isotope composition (Schroeder et al., American Journal of Physical Anthropology, 2009, 139:547–557). All other individuals present a very homogenous Pb isotope composition, which overlaps with that of British Pb sources. Conclusion: Our results indicate that while Pb isotope analyses can help identify and further characterize the sources of anthropogenic Pb in plantation settings, they might not be suited for identifying the origins of African‐born individuals in diasporic contexts.

Background Coastal environments are dynamic and rapidly changing. Living organisms in coastal environments are known to synthesise large quantities of organic osmolytes, which they use to cope with osmotic stresses. The organic osmolyte glycine betaine (GBT) is ubiquitously found in marine biota from prokaryotic Bacteria and Archaea to coastal plants, marine protozoa, and mammals. In intertidal coastal sediment, GBT represents an important precursor of natural methane emissions and as much as 90% of total methane production in these ecosystems can be originated from methanogenesis from GBT and its intermediate trimethylamine through microbial metabolism. Results We set out to uncover the microorganisms responsible for methanogenesis from GBT using stable isotope labelling and metagenomics. This led to the recovery of a near-complete genome (2.3 Mbp) of a novel clostridial bacterium involved in anaerobic GBT degradation. Phylogenetic analyses of 16S rRNA gene, functional marker genes, and comparative genomics analyses all support the establishment of a novel family Candidatus ‘Betainaceae’ fam. nov. in Clostridiales and its role in GBT metabolism. Conclusions Our comparative genomes and metagenomics analyses suggest that this bacterium is widely distributed in coastal salt marshes, marine sediments, and deep subsurface sediments, suggesting a key role of anaerobic GBT metabolism by this clostridial bacterium in these ecosystems. Electronic supplementary material The online version of this article (10.1186/s40168-019-0732-4) contains supplementary material, which is available to authorized users.

Volatile organic compounds (VOCs) are potential biomarkers for diagnosing colorectal cancer (CRC). We characterized urinary VOCs from CRC patients, their spouses/cohabitors (spouses) and first-degree relatives (relatives) to determine any differences. Correlation with stool-derived microbiomes was also undertaken.Urine from 56 CRC patients, 45 spouses and 37 relatives was assayed using liquid chromatography, field asymmetric ion mobility spectrometry (FAIMS), mass spectrometer technology. Analysis was performed using five-fold cross-validation and a random forest classifier. Faecal microbiome 16S rRNA was sequenced using Illumina MiSeq protocols and analysed using UPARSE and QIIME pipelines. VOC and microbiome profiles were also compared before and after cancer treatment.Urinary VOC profiles of CRC patients were indistinguishable from either spouses or relatives. When spouses and relatives were grouped together to form a larger non-cancer control group (n = 82), their VOC profiles became distinguishable from those of CRC patients (n = 56) with 69% sensitivity and specificity, area under the curve 0.72 (P 0.001). Microbiome analysis identified 1300 operational taxonomic units across all groups. The analysis of similarity R value was 0.067 (P 0.001), with significantly different bacterial abundances in 82 operational taxonomic units (6.2%) by Kruskal-Wallis testing. CRC patients' VOC or stool microbiome profiles were unchanged after treatment.Although CRC patients' urinary VOC profiles cannot be differentiated from those of spouses or relatives they can be differentiated from a larger non-cancer control group. Comparison of the groups' microbiomes confirmed differences in bacterial species abundance. The current FAIMS-based assay can detect a unique, but modest, signal in CRC patients' urinary VOCs, which remains unaltered after treatment.

Background: The population of Roman Britain are renowned for having elevated nitrogen (δ15) stable isotope values, which have been interpreted as evidence for the increased consumption of marine products. However, such results are now understood to also reflect episodes of stress and disease, suggesting that new interpretations are warranted. Aim: To test our novel approach which combines hazard mortality analysis and stable isotope data to determine whether there is a relationship between age-at-death, elevated δ15N values and mortality risk. Subjects and methods: We used published osteological and dietary stable isotope data for nitrogen (δ15N) and carbon (δ13C) of 659 1st-5th century AD individuals aged >12 years old excavated from Roman cemeteries in Britain. The relationship between diet and mortality risk was assessed using the Gompertz hazard model, and differences in median reported isotope values between the sexes was determined using a Mann Whitney test. Results: We discovered that higher δ15N are associated with elevated risks of mortality, whereas the opposite pattern was observed for δ13C, and males had higher median δ13C and δ15N values. Conclusion: We successfully demonstrated that stable isotope data can be integrated in to hazard models, allowing us to connect diet and mortality in past populations. It supports the findings of other isotope studies, which have established that individuals with childhood stress/trauma will have different isotope patterns.

A rescue excavation in the Chapel of the Presbyterian Church of Soly, explored a grave of two men in an unusual position among 20 other child burials in 2008–2009. The burial is dated to the early modern (16–17th century CE) Period. The 45–50-year-old males showed signs of poor health condition and both had healed fractures and perimortem sharp force traumas including also injuries due to decapitation. Craniometric and morphological features suggested the two men of non-Hungarian origin but show similar characteristics to incoming populations from South Slavic areas during the Ottoman Period of Hungary (16–17th centuries). Strontium and oxygen isotope analyses were conducted, with O isotope ratios suggested that Skeleton 12 had a non-local childhood, with a ratio consistent with an origin further east in Europe. The ratio of the sample from Skeleton 11 was consistent with a local origin but also with a wide range of other places in Central and Eastern Europe. The two men are inferred to be non-local victims of murder or extra-judicial punishment and exemplify the high level of local conflicts in this troubled Period of Hungarian history.

Fine-resolution sampling of pollen, non-pollen palynomorphs and microcharcoal as well as sedimentological data in a 6-m sediment core were used to reconstruct both natural conditions and human impacts in the late fifth and early fourth millennia cal bc in the environs of the Nebelivka megasite in Kirovograd Oblast, Central Ukraine. This 238-ha site, dating to the Middle (or BII) Phase of the Trypillia culture, represents one of the first low-density urban establishments in Europe. Despite what was believed to be a sizable population, local human impacts reconstructed from the multi-proxy palaeo-ecological record were moderate in character. There was no positive evidence to indicate a depositional hiatus in the P1 core and no sign of a major ecological impact at any stage in the high-resolution record. The palaeo-ecological record indicates modest settlement agglomeration with less permanent populations rather than permanent populations of tens of thousands of people.

Bacteriophage possess a variety of auxiliary metabolic genes (AMGs) of bacterial origin. These proteins enable them to maximise infection efficiency, subverting bacterial metabolic processes for the purpose of viral genome replication and synthesis of the next generation of virion progeny. Here, we examined the enzymatic activity of a cyanophage MazG protein – a putative pyrophosphohydrolase previously implicated in regulation of the stringent response via reducing levels of the central alarmone molecule (p)ppGpp. We demonstrate however, that the purified viral MazG shows no binding or hydrolysis activity against (p)ppGpp. Instead, dGTP and dCTP appear to be the preferred substrates of this protein, consistent with a role preferentially hydrolysing deoxyribonucleotides from the high GC content host Synechococcus genome. This showcases a new example of the fine‐tuned nature of viral metabolic processes.\ud

Vibrio campbellii is widely distributed in the marine environment and is an important pathogen of aquatic organisms such as shrimp, fish, and mollusks. The emergence of multi-drug resistance among these bacteria resulted in a worldwide public health problem, which requires alternative treatment approaches such as phage therapy. In the present study, we isolated a phage vB_Vc_SrVc2 from white shrimp hepatopancreas with symptoms of AHPND. Phage vB_Vc_SrVc2 is a member of the genus Maculvirus and the family Autographiviridae, with high lytic ability against Vibrio isolates. Phage has a high resistance to a broad range of temperatures, salinity, UV radiation and chloroform. The genome size was 43,157 bp, with a GC content of 49.2% that encodes 49 putative ORFs, no tRNAs, showed three single nucleotide polymorphisms, two small deletions and one nucleotide insertion compared to SrVc9, showing slightly different infectivity profiles.. No lysogeny related genes were detected in vB_Vc_SrVc2 genome. Overall phage vB_Vc_SrVc2 has a good potential for therapeutic use in the aquaculture industry against V. campbellii infections.

BackgroundIn order to optimize phage therapy, we need to understand how bacteria evolve against phage attack. One of the main problems of the phage therapy is the appearance of bacterial resistance variants. The use of genomics to track antimicrobial resistance is increasingly developed and used in clinical laboratories. For that reason, it is important to consider, in an emerging future with phage therapy, to detect and avoid phage resistant strains, that can be overcomed by the analysis of metadata provided by WGS. Here, we identified genes associated with phage resistance in 18 Acinetobacter baumannii clinical strain belonging to the ST-2 clonal complex during a decade (Ab2000 vs 2010): 9 from 2000 and 9 from 2010.ResultsThe presence of genes putatively associated to phage resistance were detected. Genes detected were associated with an abortive infection system, restriction-modification system, genes predicted to be associated with defence systems but with unknown function and CRISPR-Cas system. Between 118 and 171 genes were found in the 18 clinical strains. On average, 26% of these genes were detected inside genomic islands (GIs) in the 2000 strains and 32% in 2010 strains. Furthermore, 38 potential CRISPR arrays in 17 of 18 of the strains were found, as well as 705 proteins associated with CRISPR-Cas systems.ConclusionsA moderately higher presence of these genes in the strains of the 2010 in comparison to those of the 2000 were found, especially those related to the R-M system and CRISPR-Cas system. The presence of these genes in GIs in a higher rate in the strains of the 2010 compared to those of the 2000 was also detected. WGS and bioinformatics could be powerful tools to avoid drawbacks when a personalized therapy is applied. In this study, it allows us to take care of the phage resistance in A. baumannii clinical strains to prevent a failure in a possible phage therapy.

Salmonella Typhimurium carrying the multidrug resistance (MDR) plasmid pMG101 was isolated from three burns patients in Boston United States in 1973. pMG101 was transferrable into other Salmonella spp. and Escherichia coli hosts and carried what was a novel and unusual combination of AMR genes and silver resistance. Previously published short-read DNA sequence of pMG101 showed that it was a 183.5Kb IncHI plasmid, where a Tn7-mediated transposition of pco/sil resistance genes into the chromosome of the E. coli K-12 J53 host strain had occurred. We noticed differences in streptomycin resistance and plasmid size between two stocks of E. coli K-12 J53 pMG101 we possessed, which had been obtained from two different laboratories (pMG101-A and pMG101-B). Long-read sequencing (PacBio) of the two strains unexpectedly revealed plasmid and chromosomal rearrangements in both. pMG101-A is a non-transmissible 383Kb closed-circular plasmid consisting of an IncHI2 plasmid sequence fused to an IncFI/FIIA plasmid. pMG101-B is a mobile closed-circular 154 Kb IncFI/FIIA plasmid. Sequence identity of pMG101-B with the fused IncFI/IncFIIA region of pMG101-A was >99%. Assembled host sequence reads of pMG101-B showed Tn7-mediated transposition of pco/sil into the E. coli J53 chromosome between yhiM and yhiN. Long read sequence data in combination with laboratory experiments have demonstrated large scale changes in pMG101. Loss of conjugation function and movement of resistance genes into the chromosome suggest that even under long-term laboratory storage, mobile genetic elements such as transposons and insertion sequences can drive the evolution of plasmids and host. This study emphasises the importance of utilising long read sequencing technologies of plasmids and host strains at the earliest opportunity.

Megaphages – bacteriophages harbouring extremely large genomes – have recently been found to be ubiquitous, being described from a variety of microbiomes ranging from the animal gut to soil and freshwater systems. However, no complete marine megaphage has been identified to date. Here, using both short and long read sequencing, we assembled >900 high-quality draft viral genomes from water in the English Channel. One of these genomes included a novel megaphage, Mar_Mega_1 at >650 Kb, making it one of the largest phage genomes assembled to date. Utilising phylogenetic and network approaches, we found this phage represents a new family of bacteriophages. Genomic analysis showed Mar_Mega_1 shares relatively few homologues with its closest relatives, but, as with other mega-phages Mar_Mega_1 contained a variety of auxiliary metabolic genes responsible for carbon metabolism and nucleotide biosynthesis, including isocitrate dehydrogenase [NADP] and nicotinamide-nucleotide amidohydrolase [PncC] which have not previously been identified in megaphages. The results of this study indicate that phages containing extremely large genomes can be found in abundance in the marine environment and augment host metabolism by mechanisms not previously described.

Phage therapy recently passed a key milestone with success of the first regulated clinical trial using systemic administration. In this single-arm non-comparative safety study, phages were administered intravenously to patients with invasive Staphylococcus aureus infections with no adverse reactions reported. Here, we examined features of 78 lytic S. aureus phages, most of which were propagated using a S. carnosus host modified to be broadly susceptible to staphylococcal phage infection. Use of this host eliminates the threat of contamination with staphylococcal prophage — the main vector of S. aureus horizontal gene transfer. We determined the host range of these phages against an international collection of 185 S. aureus isolates with 56 different multilocus sequence types that included multiple representatives of all epidemic MRSA and MSSA clonal complexes. Forty of our 78 phages were able to infect > 90% of study isolates, 15 were able to infect > 95%, and two could infect all 184 clinical isolates, but not a phage-resistant mutant generated in a previous study. We selected the 10 phages with the widest host range for in vitro characterization by planktonic culture time-kill analysis against four isolates:- modified S. carnosus strain TM300H, methicillin-sensitive isolates D329 and 15981, and MRSA isolate 252. Six of these 10 phages were able to rapidly kill, reducing cell numbers of at least three isolates. The four best-performing phages, in this assay, were further shown to be highly effective in reducing 48 h biofilms on polystyrene formed by eight ST22 and eight ST36 MRSA isolates. Genomes of 22 of the widest host-range phages showed they belonged to the Twortvirinae subfamily of the order Caudovirales in three main groups corresponding to Silviavirus, and two distinct groups of Kayvirus. These genomes assembled as single-linear dsDNAs with an average length of 140 kb and a GC content of c. 30%. Phages that could infect > 96% of S. aureus isolates were found in all three groups, and these have great potential as therapeutic candidates if, in future studies, they can be formulated to maximize their efficacy and eliminate emergence of phage resistance by using appropriate combinations.

International audience; Evolution of virulence traits from adaptation to environmental niches other than the host is probably a common feature of marine microbial pathogens, whose knowledge might be crucial to understand their emergence and pathogenetic potential. Here we report genome sequence analysis of a novel marine bacterial species, Vibrio bathopelagicus sp. nov., isolated from warm bathypelagic waters (3309m depth) of the Mediterranean Sea. Interestingly, V. bathopelagicus sp. nov. is closely related to coastal Vibrio strains pathogenic to marine bivalves. V. bathopelagicus sp. nov. genome encodes genes involved in environmental adaptations to the deep-sea but also in virulence, such as the R5.7 element, MARTX toxin cluster, Type VI secretion system and zinc-metalloprotease, previously associated with Vibrio infection in farmed oysters. The results of functional in vitro assays on immunocytes (hemocytes) of the Mediterranean mussel Mytilus galloprovincialis and the Pacific oyster Crassostrea gigas, and of the early larval development assay in Mytilus support strong toxicity of V. bathopelagicus sp. nov. towards bivalves. V. bathopelagicus sp. nov., isolated from a remote Mediterranean bathypelagic site, is an example of a planktonic marine bacterium with genotypic and phenotypic traits associated with animal pathogenicity, that might have played an evolutionary role in the origin of coastal marine pathogens.

Human mobility and migration are thought to have played essential roles in the consolidation and expansion of sedentary villages, long-distance exchanges and transmission of ideas and practices during the Neolithic transition of the Near East. Few isotopic studies of human remains dating to this early complex transition offer direct evidence of mobility and migration. The aim of this study is to identify first-generation non-local individuals from Natufian to Pre-Pottery Neolithic C periods to explore the scope of human mobility and migration during the Neolithic transition in the Southern Levant, an area that is central to this historical process. The study adopted a multi-approach resorting to strontium (87Sr/86Sr), oxygen (δ18OVSMOW) and carbon (δ13C) isotope ratio analyses of tooth enamel of 67 human individuals from five sites in Jordan, Syria, and Israel. The isotope ratios point both to a significant level of human migration and/or mobility in the Final Natufian which is compatible with early sedentarism and seasonal mobility and with population aggregation in early sedentary hamlets. The current findings, in turn, offer evidence that most individuals dating to the Pre-Pottery Neolithic were local to their respective settlements despite certain evidence of non-locals. Interestingly, isotopic data suggest that two possible non-local individuals benefitted from particular burial practices. The results underscore a decrease in human mobility and migration as farming became increasingly dominant among the subsistence strategies throughout the Neolithic transition of the Southern Levant., The study was supported by a grant from the Marie Skłodowska-Curie Actions (European Commission, no. GA 750460; H2020-MSCA-IF-2016). In addition, this research was supported by the European Commission (Grant ERC-2019-StG 851733), the Spanish Ministry of Science, Innovation and Universities (Grant RTI2018-101923-J-I00, Grant RYC2019-028346-I and Grant HAR2016-74999-P), and Palarq Foundation. We would like to warmly thank François Valla and Hamoudi Khalaily who have given us permission to work on the anthropological collections of Mallaha.

BackgroundWith advances in sequencing technology and decreasing costs, the number of bacteriophage genomes that have been sequenced has increased markedly in the last decade.Materials and MethodsWe developed an automated retrieval and analysis system for bacteriophage genomes, INPHARED (https://github.com/RyanCook94/inphared), that provides data in a consistent format.ResultsAs of January 2021, 14,244 complete phage genomes have been sequenced. The data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated only on 30 bacterial genera. There is further bias with significantly more lytic phage genomes than temperate within the database, resulting in ~54% of temperate phage genomes originating from just three host genera. Within phage genomes, putative antibiotic resistance genes were found in higher frequencies in temperate phages than lytic phages.ConclusionWe provide a mechanism to reproducibly extract complete phage genomes and highlight some of the biases within this data, that underpins our current understanding of phage genomes.