Microbiology

Article commentary

Editors can now comment on articles published in PeerJ and elsewhere.

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota (2018) PeerJ

Konstantinos Kormas –– Sampling and handling of samples is very crucial in -omics based studies and very often the necessary attention is not met in publiched works. Such studies are necessary... Read more

Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species

Editor rating: 7 / 10

Paul Tulkens –– Although Elizabethkingia may seem as a rather rare organism in terms fo human pathology, the study illustrates well the various mechanisms of resistance to a important fluoroquinolone and will be of interest to many investigators of antibacterial resistance and to clinicians using ciprofloxacin or other fluoroquinolones.
Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data

Editor rating: 9 / 10

Lesley Hoyles –– Highlights the need for careful analyses of metagenomic data when looking at closely related bacteria, and proposes a way of dealing with this. Applicable to metagenomic studies across a range of ecological niches.
A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

Editor rating: 8 / 10

Konstantinos Kormas –– A very good effort on putting together and analysing shrimp gut microbiota.
The effects of fermentation products of prebiotic fibres on gut barrier and immune functions in vitro

Editor rating: 7 / 10

Maria Cristina Albertini –– I believe that prebiotics may have an important influence of immune response. More information are needed on intestinal barrier functions and this paper can be of support.
Occurrence of virulent multidrug-resistant Enterococcus faecalis and Enterococcus faecium in the pigs, farmers and farm environments in Malaysia

Editor rating: 8 / 10

Carlos Conte-Junior –– This paper is very relevant in food microbiology.
Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates

Editor rating: 8 / 10

Daniel Lahr –– This article attempts to retrace the complex history of re-construction of the photosynthetic pathway in organisms that went through serial endosymbiosis. It is likely to be relevant to biologists working on evolution, endosymbiosis and lateral gene transfer, thus making it a broadly interesting paper.
Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments

Section Editor rating: 7 / 10

Siouxsie Wiles –– An important article that reminds us to be aware of the assumptions we make around databases and other resources we rely on.
Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation

Section Editor rating: 8 / 10

Siouxsie Wiles –– Sounds like a really interesting study to those working on plant fungal pathogens.
Epidemiology of Haemophilus parasuis isolates from pigs in China using serotyping, antimicrobial susceptibility, biofilm formation and ERIC-PCR genotyping

Editor rating: 8 / 10

Sheng Chen –– Haemophilus parasuis is a very important pathogen in animals. More studies should be encouraged in this field.
Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4

Editor rating: 9 / 10

Luciana Leite –– Multi-omics is a technique that can be applied to several fields.

Discussing these articles

New paper by @rpetit3 with @jose_sandeep @jamesmhogan @mezewudo Bacillus anthracis identification in shotgun metagenome data using k-mers. taking into account lethal toxin gene presence and false positives from close relatives https://t.co/M6huJiFUxP via @thePeerJ

The effects of fermentation products of prebiotic fibres on gut barrier and im... - Pham VT et al. - https://t.co/oMFfnOPFG0 #microbiome

A meta-analysis reveals the environmental and #host factors shaping the structure and function of the #shrimp #microbiota https://t.co/il8mxlFwsa via @thePeerJ

Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates https://t.co/BPkcQJTVdQ #protists #algae

Our latest paper is out today where we discuss issues in taxonomy errors using the Greengenes database https://t.co/nBzPwIZ0Yq @thePeerJ #microbiology #16SrRNAgene #taxonomy #Vibrio #Pseudoalteromonas @lipp_lab