Biology subjects

Fujii, N.

Publications and source records attributed to Fujii, N..

5 recordsLinked to original sources

bioRxiv2026

Gut microbiome signatures precede chronic kidney disease diagnosis in a large canine cohort

Chronic kidney disease (CKD)-associated dysbiosis is well described after diagnosis, but whether microbial changes precede clinical recognition is unclear. We integrated insurance claims, fecal and oral 16S rRNA profiles, and clinical laboratory data from companion dogs. Among 140,025 dogs, lower gut microbial diversity was associated with incident CKD after adjustment for age, sex and body size. Prediagnostic samples showed reduced evenness-related diversity, modest community shifts and seven differentially abundant genera. A five-genus score was elevated more than two years before diagnosis, although it was derived and evaluated in the same cohort and was not intended as a predictive model. In a laboratory subset, microbial changes preceded the largest increases in blood urea nitrogen and creatinine. Paired oral-gut samples showed limited exploratory associations between periodontal-associated taxa and the gut score. These findings identify microbial features associated with future claims-defined canine CKD and support independent validation and mechanistic investigation.

microbiology↗

bioRxiv2023

Unique episymbiotic relationship between Gracilibacteria and Zoogloea in activated sludge flocs in a municipal wastewater treatment plant

Among the various bacteria present in activated sludge, uncultivated Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) are ubiquitous at the class or phylum level. Patescibacteria have a highly restricted metabolic capacity and are thought to be episymbiotic/endosymbiotic or predatory. However, only a limited number of Patescibacteria and their hosts have been identified. Therefore, many Patescibacteria have not been (co-)cultured and identified by fluorescence in situ hybridization (FISH) or electron microscopy. Little is known about the morphology, metabolic potential, and hosts of Gracilibacteria (formerly GN02 or BD1-5) which belong to Patescibacteria. In our previous study, we confirmed the presence of Gracilibacteria in activated sludge and successfully recovered its high-quality genome. In this study, we designed new probes to visualize members of Gracilibacteria in activated sludge and identified its host using FISH. The FISH observations revealed that Gracilibacteria, which formed loosely associated clusters, were located within dense clusters of Zoogloea, which were dominant in the activated sludge. The metagenome-assembled genomes (MAGs) of Zoogloea possessed genes related to extracellular polymeric substance (EPS) biosynthesis, floc formation, and nutrient removal, including a polyhydroxyalkanoate (PHA) accumulation pathway. The MAGs of Gracilibacteria possessed genes associated with type IV pili, competence protein EC (ComEC), and PHA degradation, which suggests that they have a Zoogloea-dependent lifestyle in activated sludge flocs. These findings clearly indicate a new symbiotic relationship between Gracilibacteria and Zoogloea, and to the best of our knowledge, this is the first study to show this interaction.

microbiology↗

bioRxiv2022

Inositol pyrophosphate profiling reveals regulatory roles of IP6K2-dependent enhanced IP7 metabolism in enteric nervous system

Inositol pyrophosphates (PP-IPs) regulate diverse physiological processes; to better understand their functional roles, assessing their tissue-specific distribution is important. Here, we profiled PP-IP levels in mammalian organs using a novel HILIC-MS/MS protocol and discovered that the gastrointestinal tract (GIT) contained the highest levels of IP7 and its precursor IP6. Although their absolute levels in the GIT is diet-dependent, elevated IP7 metabolism still exists under dietary regimes devoid of exogenous IP7. Of the major GIT cells, enteric neurons selectively express the IP7-synthesizing enzyme IP6K2. IP6K2-knockout mice exhibited significantly impaired IP7 metabolism in the various organs including the proximal GIT. Additionally, HILIC-MS/MS analysis displayed that genetic ablation of IP6K2 significantly impaired IP7 metabolism in the gut and duodenal muscularis externa containing myenteric plexus. Whole transcriptome analysis of duodenal muscularis externa further suggested that IP6K2 inhibition induced the gene sets associated with mature neurons such as inhibitory, GABAergic and dopaminergic neurons, concomitantly with suppression of those for neural progenitor/stem cells and glial cells. In addition, IP6K2 inhibition explicitly affected transcript levels of certain genes modulating neuronal differentiation and functioning, implying critical roles of IP6K2-IP7 axis in developmental and functional regulation of enteric nervous system. These results collectively reveal an unexpected role of mammalian IP7--a highly active IP6K2-IP7 pathway is conducive to enteric nervous system.

molecular biology↗

bioRxiv2019

Broadband Signal Rather than Frequency-Specific Rhythms Underlies Prediction Error in the Primate Auditory Cortex

Detection of statistical irregularities, measured as a prediction error response, is fundamental to the perceptual monitoring of the environment. We studied whether prediction error response is associated with neural oscillations or asynchronous broadband activity. Electrocorticography (ECoG) was carried out in three male monkeys, who passively listened to the auditory roving oddball stimuli. Local field potentials (LFP) recorded over the auditory cortex underwent spectral principal component analysis, which decoupled broadband and rhythmic components of the LFP signal. We found that the broadband component captured the prediction error response, whereas none of the rhythmic components were associated with statistical irregularities of sounds. The broadband component displayed more stochastic, asymmetrical multifractal properties than the rhythmic components, which revealed more self-similar dynamics. We thus conclude that the prediction error response is captured by neuronal populations generating asynchronous broadband activity, defined by irregular dynamical states which, unlike oscillatory rhythms, appear to enable the neural representation of auditory prediction error response. Significance StatementThis study aimed to examine the contribution of oscillatory and asynchronous components of auditory local field potentials in the generation of prediction error responses to sensory irregularities, as this has not been directly addressed in the previous studies. Here, we show that mismatch negativity - an auditory prediction error response - is driven by the asynchronous broadband component of potentials recorded in the auditory cortex. This finding highlights the importance of non-oscillatory neural processes in the predictive monitoring of the environment. At a more general level, the study demonstrates that stochastic neural processes, which are often disregarded as neural noise, do have a functional role in the processing of sensory information.

neuroscience↗

bioRxiv2018

EECoG-Comp: An Open Source Platform for Concurrent EEG/ECoG Comparisons

Electrophysiological Source Imaging (ESI) methods are hampered by the lack of "gold standards" for model comparison. Concurrent electroencephalography (EEG) and electrocorticography (ECoG) recordings (namely EECoG) are considered gold standard to validating EEG generative models with primate models have the unique advantages of both flexibility and translational value in human research. However the severe EEG artifacts during such invasive experiments, the complexity of providing sufficiently detailed biophysical models, as well as lacking sound statistical connectivity comparison methods have hampered the availability and analysis of such datasets. In this paper, 1) we provide EECoG-Comp: an open source platform (https://github.com/Vincent-wq/EECoG-Comp) which encompasses the preprocessing, forward modeling, simulation and comparison module; 2) we take the simultaneous EECoG dataset from www.neurotycho.org as an example to illustrate the use of this platform and compare the source connectivity estimation performance of 4 popular ESI methods named MNE, LCMV, eLORETA and SSBL. The conclusion shows the limits of performance of these ESI connectivity estimators using both simulations and real data analysis. In fact, the use of this platform also suggests the need for both improved simultaneous EEG and ECoG experiments and ESI connectivity estimators.

bioinformatics↗