Abstract
Microbial
pangenome
analysis
identifies
present
or
absent
genes
in
prokaryotic
genomes.
However,
current
tools
are
limited
when
analyzing
species
with
higher
sequence
diversity
taxonomic
orders
such
as
genera
families.
The
Roary
ILP
Bacterial
core
Annotation
Pipeline
(RIBAP)
uses
an
integer
linear
programming
approach
to
refine
gene
clusters
predicted
by
for
identifying
genes.
RIBAP
successfully
handles
the
complexity
and
of
Chlamydia
,
Klebsiella
Brucella
Enterococcus
genomes,
outperforming
other
established
recent
all-encompassing
at
genus
level.
is
a
freely
available
Nextflow
pipeline
github.com/hoelzer-lab/ribap
zenodo.org/doi/10.5281/zenodo.10890871.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2025,
Номер
75(1)
Опубликована: Янв. 21, 2025
A
clinical
isolate,
R131,
was
isolated
from
the
peritoneal
swab
of
a
patient
who
suffered
ruptured
appendicitis
with
abscess
and
gangrene
in
Hong
Kong
2018.
Cells
are
facultatively
anaerobic,
non-motile,
Gram-positive
coccobacilli.
Colonies
were
small,
grey,
semi-translucent,
low
convex
alpha-haemolytic.
The
bacterium
grew
on
blood
agar
but
not
Brain
Heart
Infusion
(BHI)
Mueller–Hinton
agars.
It
negative
for
catalase,
oxidase,
indole
aesculin
hydrolysis.
initial
identification
attempts
via
matrix-assisted
laser
desorption
ionization–time
flight
mass
spectrometry
16S
rRNA
gene
sequencing
yielded
inconclusive
results.
analysis
showed
that
R131
shared
>99%
nucleotide
identity
certain
uncultured
Actinomycetales
bacteria.
In
this
retrospective
investigation,
complete
genome
constructed,
disclosing
DNA
G+C
content
64%.
Phylogenetic
mostly
related
to
Scrofimicrobium
canadense
WB03_NA08,
which
first
described
2020.
However,
its
only
94.15%
S.
WB03_NA08.
Notably,
orthoANI
between
WB03_NA08
67.81%.
pan-genome
encompassing
4
genomes
986
core
clusters
species,
along
601
cloud
genes.
average
comparisons
within
ranged
59.78
62.51%
other
species.
Correspondingly,
dDDH
values
19.20
22.30%,
while
POCP
spanned
57.48
60.94%.
Therefore,
novel
appendicitidis
sp.
nov.,
is
proposed.
type
strain
T
(=JCM
36615
=LMG
33627
).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2025,
Номер
75(3)
Опубликована: Март 13, 2025
Five
yeast
isolates
belonging
to
a
candidate
for
novel
species
were
obtained
from
rotting
wood
and
the
gut
of
passalid
beetle
larva
in
site
Amazonian
rainforest
biome
Brazil.
Sequence
analysis
Internal
Transcribed
Spacer
(ITS)-5.8S
region
D1/D2
domains
large
subunit
rRNA
gene
showed
that
represent
genus
Vanderwaltozyma
.
The
closest
relative
is
huisunica
These
differs
due
44
nt
substitutions
21
indels
sequences
ITS
region,
as
well
by
15
four
domains.
A
phylogenomic
with
genomes
sequenced
this
an
outgroup
other
genus.
We
propose
name
urihicola
sp.
nov.
(CBS
18107
T
,
MycoBank
MB
856975)
accommodate
these
isolates.
homothallic,
producing
one
two
ascospores
per
ascus.
habitat
V.
Brazilian
biome.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2025,
Номер
75(3)
Опубликована: Март 28, 2025
Phylogenetic
analysis
of
the
genus
Aureimonas
,
utilizing
both
16S
rRNA
gene
sequences
and
comprehensive
whole-genome
data,
revealed
its
polyphyletic
nature,
necessitating
a
revision
to
accommodate
phylogenetically
distinct
species.
Based
on
established
threshold
values
for
demarcation
–
specifically,
similarity,
Average
Amino
Acid
Identity
Percentage
Conserved
Proteins
notably
substantial
divergence
was
observed
within
division
into
four
genera
is
strongly
supported.
To
address
this,
we
propose
establishment
new
genera:
Dennerimonas
gen.
nov.,
Mesocryomonas
Rathsackimonas
nov.
Plantimonas
These
classifications
species
that
are
significantly
divergent
from
type
thereby
more
accurately
reflecting
their
evolutionary
lineages.
Additionally,
glaciistagni
proposed
be
reclassified
Jiella
as
comb.
based
phylogenetic
evidence
indicating
closer
relationship
than
other
members
.
Our
analysis,
which
included
assessments
Nucleotide
Identity,
digital
DNA–DNA
hybridization
exceeding
delineation
thresholds,
further
supports
reclassification
Jeongeupella
Jiang
et
al
2024
later
heterotypic
synonym
Antarcticirhabdus
Du
2023.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2025,
Номер
75(4)
Опубликована: Апрель 16, 2025
A
Gram-negative
bacterial
strain,
designated
ACPt
T
,
was
isolated
from
the
top
of
covering
soil
an
active
charcoal-burning
pile.
The
cells
were
strictly
anaerobic,
rod-shaped
and
grew
optimally
at
40
°C
pH
7.
substrates
ribose,
glucose,
sucrose,
raffinose,
melezitose,
pyruvate,
vanillate,
syringate,
methanol
CO
utilized
for
growth.
Phylogenomic
analysis
4.1
Mb
genome
showed
that
strain
represented
a
novel
species
genus
Sporomusa
.
most
closely
related
to
malonica,
with
average
amino
acid
identity
80.1%.
encoded
cytochromes,
ubiquinones,
Wood–Ljungdahl
gene
cluster
Rnf
complex,
which
identified
as
common
features
all
type
strains.
However,
did
not
ferment
H
2
+CO
via
acetogenesis
other
but
employed
metabolism
carboxydotrophic
hydrogenogen,
converting
Based
on
genomic,
morphological
physiological
presented
in
this
study,
is
proposed
Sporomusa,
name
carbonis
sp.
nov.
(DSM
116159
CCOS
2105
).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY,
Год журнала:
2024,
Номер
74(10)
Опубликована: Окт. 21, 2024
Acetic
acid
bacteria
–
belonging
to
the
Acetobacteraceae
family
are
found
in
gut
of
many
sugar-feeding
insects.
In
this
study,
six
strains
have
been
isolated
from
hemipteran
leafhopper
Euscelidius
variegatus
.
While
they
exhibit
high
16S
rRNA
gene
sequence
similarities
uncultured
members
family,
could
not
be
unequivocally
assigned
any
particular
type
species.
Considering
clonality
isolates,
EV16P
T
strain
was
used
as
a
representative
group
isolates.
The
genome
is
composed
2.388
Mbp
chromosome,
with
DNA
G+C
content
57
mol%.
Phylogenetic
analyses
based
on
and
whole-genome
multilocus
analysis
indicate
that
forms
monophyletic
clade
uncultivated
endosymbiont
Diaphorina
citri
,
Candidatus
Kirkpatrickella
diaphorinae.
Such
phylogenetic
positioned
between
those
Asaia-Swaminathania
Kozakia
genomic
distance
metrics
protein
sequences
support
proposal
new
species
yet-undescribed
genus.
It
rod-shaped
Gram-stain-negative
bacterium,
strictly
aerobic,
non-motile,
non-spore-forming,
showing
optimal
growth
without
salt
(NaCl)
at
30
°C
pH
6–7.
major
quinone
Q10,
dominant
cellular
fatty
acids
(>10%)
C
18:l
ω
7c,
19
:
0
cyclo
6c,
16
1
2OH.
polar
lipid
profile
comprises
diphosphatidylglycerol,
phosphatidylethanolamine
phosphatidylcholine,
along
unidentified
aminophospholipids,
glycophospholipids,
aminolipids
lipids.
Based
polyphasic
approach,
including
phylogenetic,
phylogenomic,
relatedness,
phenotypic
chemotaxonomic
characterisations,
(=
KCTC
8296
=
DSM
117028
)
proposed
novel
genus
name
Sorlinia
euscelidii
gen.
nov.,
sp.
honour
Prof.
Claudia
Sorlini,
an
Italian
environmental
microbiologist
University
Milan
who
inspired
research
microbial
diversity,
symbiosis
plants
animals.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Июнь 21, 2024
Abstract
A
Gram-negative
bacterial
strain,
designated
ACPt
T
,
was
isolated
from
the
covering
top
soil
of
an
active
charcoal
burning
pile.
Cells
were
strictly
anaerobic,
rod-shaped
and
grew
optimally
at
40°C
pH
7.
The
substrates
ribose,
glucose,
sucrose,
raffinose,
melezitose,
pyruvate,
vanillate,
syringate,
methanol
CO
utilized
for
growth.
Phylogenomic
analysis
4.1
Mb
genome
showed
that
strain
represented
a
novel
species
genus
Sporomusa
.
most
closely
related
to
malonica
with
average
amino
acid
identity
80.1%.
encoded
cytochromes,
ubiquinones,
Wood-Ljungdahl
gene
cluster
Rnf
complex,
which
identified
as
common
features
all
type
strains.
However,
did
not
ferment
H
2
+
via
acetogenesis
other
species,
but
employed
metabolism
carboxydotrophic
hydrogenogen
converting
Based
on
genomic,
morphological
physiological
presented
in
this
study,
is
proposed
name
carbonis
sp.
nov.
(DSM
116159
CCOS
2105
).
