The integrated stress response promotes neural stem cell survival under conditions of mitochondrial dysfunction in neurodegeneration

Impaired mitochondrial function is a hallmark of aging and a major contributor to neurodegenerative diseases. We have shown that disrupted mitochondrial dynamics typically found in aging alters the fate of neural stem cells (NSCs) leading to impairments in learning and memory. At present, little is known regarding the mechanisms by which neural stem and progenitor cells survive and adapt to mitochondrial dysfunction. Using Opa1-inducible knockout as a model of aging and neurodegeneration, we identify a decline in neurogenesis due to impaired stem cell activation and progenitor proliferation, which can be rescued by the mitigation of oxidative stress through hypoxia. Through sc-RNA-seq, we identify the ATF4 pathway as a critical mechanism underlying cellular adaptation to metabolic stress. ATF4 knockdown in Opa1-deficient NSCs accelerates cell death, while the increased expression of ATF4 enhances proliferation and survival. Using a Slc7a11 mutant, an ATF4 target, we show that ATF4-mediated glutathione production plays a critical role in maintaining NSC survival and function under stress conditions. Together, we show that the activation of the integrated stress response (ISR) pathway enables NSCs to adapt to metabolic stress due to mitochondrial dysfunction and metabolic stress and may serve as a therapeutic target to enhance NSC survival and function in aging and neurodegeneration.

Early postnatal defects in neurogenesis in the 3xTg mouse model of Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder leading to dementia. The hippocampus, which is one of the sites where neural stem cells reside and new neurons are born, exhibits the most significant neuronal loss in AD. A decline in adult neurogenesis has been described in several animal models of AD. However, the age at which this defect first appears remains unknown. To determine at which stage, from birth to adulthood, the neurogenic deficits are found in AD, we used the triple transgenic mouse model of AD (3xTg). We show that defects in neurogenesis are present as early as postnatal stages, well before the onset of any neuropathology or behavioral deficits. We also show that 3xTg mice have significantly fewer neural stem/progenitor cells, with reduced proliferation and decreased numbers of newborn neurons at postnatal stages, consistent with reduced volumes of hippocampal structures. To determine whether there are early changes in the molecular signatures of neural stem/progenitor cells, we perform bulk RNA-seq on cells sorted directly from the hippocampus. We show significant changes in the gene expression profiles at one month of age, including genes of the Notch and Wnt pathways. These findings reveal impairments in neurogenesis very early in the 3xTg AD model, which provides new opportunities for early diagnosis and therapeutic interventions to prevent neurodegeneration in AD.

Corynebacterium neomassiliense sp. nov., a new bacterium isolated in a stool sample from a healthy male pygmy

An obligate aerobic, Gram-positive, non-sporulating, rod-shaped bacterium designated Marseille P3888T was isolated from the stool sample of a healthy male pygmy. We described its main characteristics, and sequenced and annotated its genome. The 16S rRNA analysis revealed 98.10% sequence similarity with Corynebacterium terpenotabidum, the phylogenetically closest species with standing in nomenclature. The genome had a size of 3142051 bp with a guanine + cytosine content of 66.83%. We proposed the creation of the new Corynebacterium neomassiliense sp. nov. strain Marseille-P3888T.

Anaerosphaera massiliensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy

Anaerosphaera massiliensis strain Marseille-P4592T (= CSURP4592T; = CCUG72452T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo.

Enterococcus mediterraneensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy

Enterococcus mediterraneensis strain Marseille-P4358T (= CSURP4358T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo.

Corrigendum to 'Phoenicibacter congonensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman

[This corrects the article DOI: 10.1016/j.nmni.2017.04.003.].

Lactate is an antidepressant that mediates resilience to stress by modulating the hippocampal levels and activity of histone deacetylases

Chronic stress promotes depression in some individuals, but has no effect in others. Susceptible individuals exhibit social avoidance and anxious behavior and ultimately develop depression, whereas resilient individuals live normally. Exercise counteracts the effects of stress. Our objective was to examine whether lactate, a metabolite produced during exercise and known to reproduce specific brain exercise-related changes, promotes resilience to stress and acts as an antidepressant. To determine whether lactate promotes resilience to stress, male C57BL/6 mice experienced daily defeat by a CD-1 aggressor, for 10 days. On the 11th day, mice were subjected to behavioral tests. Mice received lactate before each defeat session. When compared with control mice, mice exposed to stress displayed increased susceptibility, social avoidance and anxiety. Lactate promoted resilience to stress and rescued social avoidance and anxiety by restoring hippocampal class I histone deacetylase (HDAC) levels and activity, specifically HDAC2/3. To determine whether lactate is an antidepressant, mice only received lactate from days 12-25 and a second set of behavioral tests was conducted on day 26. In this paradigm, we examined whether lactate functions by regulating HDACs using co-treatment with CI-994, a brain-permeable class I HDAC inhibitor. When administered after the establishment of depression, lactate behaved as antidepressant. In this paradigm, lactate regulated HDAC5 and not HDAC2/3 levels. On the contrary, HDAC2/3 inhibition was antidepressant-like. This indicates that lactate mimics exercise's effects and rescues susceptibility to stress by modulating HDAC2/3 activity and suggests that HDAC2/3 play opposite roles before and after establishment of susceptibility to stress.

Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum

Enterococcus timonensis sp. nov., strain Marseille-P2817^T, is a facultatively anaerobic, motile and non-spore-forming Gram-positive coccus which was isolated from the sputum of a healthy adult man in Marseilles. We present herein its phenotypic description together with MALDI-TOF (matrix-assisted laser-desorption/ionization time-of-flight) mass spectrometry analysis and genome sequencing and comparison. The genome of Enterococcus timonensis is 2 123 933 bp long with 38.46 mol% of G+C content, and it contains 1983 protein-coding genes and 65 RNA genes (including nine rRNA genes).

Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards.

Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics

Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.

Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics

The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.

Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples

We present the description of Sanguibacter massiliensis sp. nov., Actinomyces minihominis sp. nov., Clostridium minihomine sp. nov., Neobittarella massiliensis gen. nov. and Miniphocibacter massiliensis gen. nov., new bacterial species isolated by culturomics from human stool samples.

'Enterococcus timonensis' sp. nov., 'Actinomyces marseillensis' sp. nov., 'Leptotrichia massiliensis' sp. nov., 'Actinomyces pacaensis' sp. nov., 'Actinomyces oralis' sp. nov., 'Actinomyces culturomici' sp. nov. and 'Gemella massiliensis' sp. nov., new bacterial species isolated from the human respiratory microbiome

We report the main characteristics of 'Enterococcus timonensis' strain Marseille-P2817T (CSUR P2817), 'Leptotrichia massiliensis' sp. nov., strain Marseille-P3007T (CSUR P3007), 'Actinomyces marseillensis' sp. nov., strain Marseille-P2818T (CSUR P2818), 'Actinomyces pacaensis' sp. nov., strain Marseille-P2985T (CSUR P2985), 'Actinomyces oralis' sp. nov., strain Marseille-P3109T (CSUR P3109), 'Actinomyces culturomici' sp. nov., strain Marseille-P3561T (CSUR P3561) and 'Gemella massiliensis' sp. nov., strain Marseille-P3249T (CSUR P3249) which were isolated from human sputum samples.

'Lactobacillus raoultii' sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis

We report the isolation of a new bacterium species, 'Lactobacillus raoultii' strain Marseille P4006 (CSUR P4006), isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis.

Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool

Strain Marseille-P3237 was isolated from a stool sample of a healthy 35-year-old Congolese pygmy female. This anaerobic, Gram-negative, non-spore-forming and non-motile coccus-shaped bacterium is a member of the order Coriobacteriales. It exhibits a 2 009 306-bp genome with a 65.46 mol% G+C content and is closely related to, but distinct from, members of the Olsenella genus. We propose the creation of the new genus Libanicoccus gen. nov. and of the new species Libanicoccus massiliensis sp. nov.

'Phoenicibacter massiliensis' gen. nov., sp. nov., a new bacterium isolated from the human gut of a pygmy woman

This study supports the main characteristics of the new genus and new species 'Phoenicibacter massiliensis' strain Marseille-P3241T (CSUR P3241), a new bacterium isolated from a stool sample of a healthy 47-year-old pygmy woman.

'Olsenella congonensis' sp.nov., identified in human stool sample

We report the main characteristics of 'Olsenella congonensis' strain Marseille-P3359T (CSUR P3359), which was isolated from the stool sample of a healthy 47-year-old pygmy female.

"Eggerthella timonensis" gen. nov. isolated from a human stool sample

We report the main characteristics of "Eggerthella timonensis" strain Marseille-P3135 which was isolated from a stool sample of a healthy 8-year-old pygmy (Baka) girl.

"Collinsella bouchesdurhonensis" sp. nov., identified in human stool sample

We report the main characteristics of "Collinsella bouchesdurhonensis" strain Marseille-P3296, which was isolated from a stool sample of a healthy 50-year-old pygmy (Baka) woman.

'Pygmaiobacter massiliensis' sp. nov., a new bacterium isolated from the human gut of a Pygmy woman

This study supports the main characteristics of a new genus 'Pygmaiobacter' and a new species 'Pygmaiobacter massiliensis' strain Marseille-P3336 (CSUR P3336); that was isolated from a stool sample of a healthy 47-year-old Pygmy woman. The Institut Fédératif de Recherche ethics committee, gave approval for this study under the number 09-022. Samples were collected for microbial content description as part of the human microbiome description by culturomics.

'Raoultibacter timonensis' gen. nov., sp. nov. , a new bacterium isolated from the human gut of a Pygmy woman

We report the main characteristics of a new species 'Raoultibacter timonensis' strain Marseille-P3277 (CSUR P3277), a new member of the genus Raoultibacter, that was isolated from a stool sample of a healthy 11-year-old Pygmy woman.

'Gabonibacter timonensis' sp. nov., a new bacterium isolated from the human gut of a Pygmy woman

This study supports the main characteristics of a new genus 'Gabonibacter timonensis' strain Marseille-P3388 (CSUR P3388); a new member of the Gabonibacter genus and Porphyromonadaceae family, that was isolated from a stool sample of a healthy 47-year-old Pygmy woman.

'Congobacterium massiliense' gen. nov. sp. nov., a new bacterium isolated from the gut of a pygmy (Baka) woman

We report the main characteristics of a new genus, 'Congobacterium,' and a new species, 'Congobacterium massiliense,' strain Marseille-P3295 (CSUR P3295), a new member in the order Coribacteriacea, which was isolated from a stool sample of a healthy 50-year-old pygmy (Baka) woman.

'Mobilibacterium massiliense' gen. nov. and 'Mobilibacterium timonense' sp. nov., identified in a human stool specimen

This study presents the main characteristics of 'Mobilibacterium massiliense' strain P2510 (CSUR P2510) and 'Mobilibacterium timonense' strain P3194 (CSUR P3194), isolated from a stool sample of a patient at the Timone hospital and from a stool sample of a healthy 50-year-old pygmy (Baka) woman, respectively.

"Libanicoccus massiliensis" gen. nov., sp. nov., a new bacterium isolated from a stool sample from a pygmy woman

This study supports the main characteristics of a new genus "Libanicoccus massiliensis" strain Marseille-P3237 (CSURP3237); a new member of the order Coribacteriaceae that was isolated from a stool sample from a healthy 35-year-old pygmy woman.