Raphael Eisenhofer
YOU?
Author Swipe
View article: Robust, Open‐Source and Automation‐Friendly <scp>DNA</scp> Extraction Protocol for Hologenomic Research
Robust, Open‐Source and Automation‐Friendly <span>DNA</span> Extraction Protocol for Hologenomic Research Open
Global efforts to standardise methodologies benefit greatly from open‐source procedures that enable the generation of comparable data. Here, we present a modular, high‐throughput nucleic acid extraction protocol standardised within the Ear…
View article: Guidelines for preventing and reporting contamination in low-biomass microbiome studies
Guidelines for preventing and reporting contamination in low-biomass microbiome studies Open
View article: The influence of season, habitat and diet on the faecal microbiome of the yellow-footed rock-wallaby (Petrogale xanthopus xanthopus)
The influence of season, habitat and diet on the faecal microbiome of the yellow-footed rock-wallaby (Petrogale xanthopus xanthopus) Open
Knowledge of an animal’s microbiome is becoming increasingly recognised as an important consideration in the conservation of threatened species, particularly in the face of wide-spread changes to climate and rainfall patterns. The yellow-f…
View article: Microbiota changes in lactation in the short-beaked echidna ( <i>Tachyglossus aculeatus</i> )
Microbiota changes in lactation in the short-beaked echidna ( <i>Tachyglossus aculeatus</i> ) Open
Monotreme and marsupial development is characterized by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functio…
View article: The bacterial community associated with the solitary resin bee <i>Megachile tosticauda</i> throughout its life cycle
The bacterial community associated with the solitary resin bee <i>Megachile tosticauda</i> throughout its life cycle Open
Unlike in eusocial bees where the identity, acquisition, and function of symbiotic microbes are well understood, little is known about the relationships formed between solitary bees and bacteria. Assessing the potential role of microbes in…
View article: Blanking on blanks: few insect microbiota studies control for contaminants
Blanking on blanks: few insect microbiota studies control for contaminants Open
Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial bi…
View article: Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide
Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide Open
Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate…
View article: The Earth Hologenome Initiative: Data Release 1
The Earth Hologenome Initiative: Data Release 1 Open
Background The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host–microbiota perspective, through the standardized generation and analysis of…
View article: Hologenomic data generation and analysis in wild vertebrates
Hologenomic data generation and analysis in wild vertebrates Open
Hologenomics, the joint analysis of host genomes and microbial metagenomes, has the potential to address fundamental biological questions from a systemic host‐microbiota perspective. However, multiple fieldwork, laboratory and bioinformati…
View article: The disciplinary matrix of holobiont biology
The disciplinary matrix of holobiont biology Open
Uniting life’s seen and unseen realms guides a conceptual advance in research
View article: Functional insights into the effect of feralisation on the gut microbiota of cats worldwide
Functional insights into the effect of feralisation on the gut microbiota of cats worldwide Open
Feralisation, the process by which domesticated organisms revert to a wild state, is a widespread phenomenon across various species. Successfully adapting to a new environment with different access to food, shelter, and other resources req…
View article: A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change
A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change Open
Coral reefs are declining worldwide due to anthropogenic-driven environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic micr…
View article: Blanking on Blanks: Few Insect Microbiota Studies Control for Contaminants - A Systematic Review
Blanking on Blanks: Few Insect Microbiota Studies Control for Contaminants - A Systematic Review Open
Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial bi…
View article: Quantifying microbial DNA in metagenomes improves microbial trait estimation
Quantifying microbial DNA in metagenomes improves microbial trait estimation Open
Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial commu…
View article: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT Open
Background Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://…
View article: A global initiative for ecological and evolutionary hologenomics
A global initiative for ecological and evolutionary hologenomics Open
View article: Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns
Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns Open
Metagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial reads in a metagenome, forcing many analysis techniques to make the often-faulty assu…
View article: Assessing the Utility of Strontium Isotopes in Fossil Dental Calculus
Assessing the Utility of Strontium Isotopes in Fossil Dental Calculus Open
Strontium (Sr) isotopes measured in fossil remains have been a useful tool to assess the geographical origin and even migrations of humans and other animals. In particular, dental enamel generally represents the ideal material, as it is de…
View article: A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics Open
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess …
View article: Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities
Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities Open
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, th…
View article: Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus)
Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus) Open
Monotreme and marsupial early development is characterised by a short gestation, the birth of the young at an early stage of development, and a long lactation in the pouch or pseudo-pouch. The lack of a functional adaptive immune system in…
View article: The prevalence of controls in phyllosphere microbiome research: a methodological review
The prevalence of controls in phyllosphere microbiome research: a methodological review Open
Summary DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over th…
View article: Quantifying microbial DNA in metagenomes improves microbial trait estimation
Quantifying microbial DNA in metagenomes improves microbial trait estimation Open
Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial commu…
View article: Assessing the utility of strontium isotopes in fossil dental calculus
Assessing the utility of strontium isotopes in fossil dental calculus Open
Strontium (Sr) isotopes measured in fossil remains have been a useful tool to assess the geographical origin and even migrations of humans and other animals. In particular, dental enamel generally provides as the ideal material, as it is d…
View article: A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics Open
Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess …
View article: Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors
Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors Open
The ability of the gut microbiome has been posited as an additional axis of animals’ phenotypic plasticity. However, whether and how such plasticity varies across hosts with different biological features remains unclear. We performed a cap…
View article: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT Open
Background : Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https…
View article: Reduced metabolic capacity of the gut microbiota associates with host growth in broiler chickens
Reduced metabolic capacity of the gut microbiota associates with host growth in broiler chickens Open
Understanding the development of functional attributes of host-associated microbial communities is essential for developing novel microbe-based solutions for sustainable animal production. We applied multi-omics to 388 broiler chicken caec…
View article: Monitoring the viable grapevine microbiome to enhance the quality of wild wines
Monitoring the viable grapevine microbiome to enhance the quality of wild wines Open
Grapevines that are used for winemaking host a diverse range of microorganisms that make up their microbiome. The microbes that inhabit the grapevine have been used by winemakers to produce wine for centuries, although modern wine producer…
View article: Pouch bacteria: an understudied and potentially important facet of marsupial reproduction
Pouch bacteria: an understudied and potentially important facet of marsupial reproduction Open
Australia is home to a rich biodiversity of marsupials that are found nowhere else. Unfortunately, many of these species are currently threatened with extinction due to introduced feral predators and other anthropogenic factors. There is g…