Micro-Library
Scientists rely on relevant and useful publications to move forward, both professionally and intellectually, but the available literature is scattered among many scientific journals and often difficult to localize. Here is a list of publications in the field of Microbiology, Metagenomics, Microbial Ecology and related, that you may find useful in chronological order with some personal comments. Note that most hyperlinks take you directly to the PDFs.
***Are you curious about the microbes above? Visit this link.
No olvides visitar nuestro blog acerca de Microorganismos en Español.
Last update: June 6, 2023
Since 2019, we started three separate sections on Ruminants, Cats and Dogs, and Birds. It is my hope that scientists in Mexico and elsewhere benefit from these sources of interesting scientific publications.
Books
1906. "The New Hygiene: Three Lectures on the Prevention of Infectious Diseases" by Elie Metchnikoff.
In the preface written by E. Ray Lankester, it reads that "some of the latest results in regard to infection, the part played by those peculiar vegetable organisms - the infective germs or bacteria - the part played by the eater-cells or phagocytes of man when attacked by such germs".
1908. "The Prolongation of Life: Optimistic studies" by Elie Metchnikoff.
One of the most interesting materials to read to get an exciting view of the thoughts about microorganisms more than a century ago.
Some examples:
Chapter IV: Intestinal putrefaction shortens life
Page 151. "The intestinal microbes are most numerous in the large intestine. This organ, which is useful to mammals the food of which consists of rough bulky vegetable matter, and which require a large reservoir for the waste of the process of digestion, is certainly useless in the case of man".
Page 156. "Is it possible, without operative interference, to take direct action against the intestinal flora by the use of antiseptics?
Page 159. "Recently, at the suggestion of Mr. Fletcher, the advantage of eating extremely slowly has been recognised, the object being to prepare for the utilisation of the food materials, and to prevent intestinal putrefaction".
Chapter V: Lactic acid as inhibiting intestinal putrefaction
Page 161. "At birth the human intestine is full, but contains no microbes"
Page 161. "The food, therefore, has an influence on the microbes of the intestine"
1926. "Cazadores de Microbios" by Paul de Kruif.
The link is to the book in Spanish.
2015. "Follow Your Gut: The Enormous Impact of Tiny Microbes" by Rob Knight.
For those of you who did not know, Rob Knight not only writes cool papers about microbial communities but also fascinating books about them!
Papers
1875
"The germ-theory of disease: being a discussion of the relation of bacteria and allied organisms to virulent inflammations and specific contagious fevers" by HC Bastian.
1876
"A word on the origin of Bacteria, and on abiogenesis" by William Roberts.
Fascinating: "Dr. Bastian has cited my name and quoted my experiments in a way that might it appear that my investigations lend some support to his views on the origin of bacteria; this is, however, not the case. On the contrary, the weight of my experiments is entirely against him and in favour of Pasteur's conclusions."
1878
"Do bacteria or their germs exist in the organs of healthy living animals?" by Chiene and Ewart.
Interesting title (?). In this paper, the authors tried to answer a very important question, which is "Are Bacteria present in the alimentary canal? Of this there can be no doubt, but that in health they can pass through the mucous membrane, and enter directly the blood stream by the veins, or indirectly by the lymphatics, we have no evidence".
"Microbes organized, their role in fermentation, putrefaction and the contagion" by Louis Pasteur.
1887
"The behaviour of Bacteria in the digestive tract" by A. Macfadyen.
1905
"On the structure and biology of the yeast plant: (Saccharomyces cerevisioe.)" by F. Mutchler.
In this paper, the author says that "Before going into a discussion of the structural elements of the yeast plant and the homologies of this structure to those of known plant and animal cells, it is thought well to refer to the structure of the most simple plants, namely, bacteria."
Also, the author says that "It is rightly maintained that the limits of a species are difficult to describe. Since the time of Linnaeus, and even before, many species have been made out and described, and year after year that catalogue becomes more extensive; yet no one has been able to give us an adequate definition of a species. Until one knows just what effect differences in environment have on a plant or animal, such a definition cannot be formulated".
1909
"The fecal bacteria of healthy man" by MacNeal et al.
This paper shows the results of a extensive survey of fecal bacteria from about 200 stool samples. This paper is also important because of the efforts placed in enumerating the microorganisms.
1911
"A method for the quantitative determination of fecal Bacteria" by Mattill and Hawk.
1914
"The contribution of bacteria to the feces after feeding diets free from indigestible components" by Thomas B. Osborne and Lafayette B. Mendel.
You simply have to read it.
1918
"Comments on the evolution and classification of Bacteria" by Breed et al.
"The characteristics of bacteria of the colon type occurring in human feces" by Rogers et al.
1922
"The source of the microorganisms in the lungs of normal animals" by Jones.
1927
"The nitrogenous constituents of hen urine" by Rusell E. Davis.
In this paper the author describes a methodology by which the urine could be collected without contamination with feces in chickens. This is important in studies of the gut microbiota in birds.
1931
"Variation and type specificity in the bacterial species Hemophilus influenzae" by Margaret Pittman.
1947
"Yeast and rickets" by E. Hoff-Jørgensen.
1948
"Further studies of the rachitogenic effect of dried yeast in pig diets" by Braude et al.
First time I hear about rickets, a condition that results in weak or soft bones in people and animals. The authors of this paper say that "in previous papers it has been described the development of rickets in fattening pigs on diets containing a large proportion of yeast, its cure or complete prevention with vitamin D, and its parttial prevention with additional calcium salts".
While this is a new topic for me, in this same paper it says that the yeast may inhibit phytase activity.
1956
"The comparative physiology and biochemistry of the blue-green algae" by GE Fogg.
"The principles of group differentiation within the Enterobacteriaceae by biochemical methods" by Kauffmann et al. In this paper, the authors said that: ‘ under these circumstances. . . it is impossible to decide whether a given classification is scientifically correct, but only whether it is more or less practical and expedient’. This reference was obtained from Sneath 1957 (see below), but I could not find the actual link to the paper sorry.
1957
"Some thoughts on bacterial classification", and
"The application of computers to taxonomy" by P.H.A. Sneath.
For those of you who enjoy biological classification.
1958
"Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium" by Schachter et al.
1961
"The faecal bacterial flora of animals and man: its development in the young" by Smith and Crabb.
This paper is very interesting but I just cannot find it in the internet anymore. I do have the PDF just in case you need it.
1962
"Histamine and 5-hydroxytryptamine in the intestinal tract of germ-free animals, animals harbouring one microbial species and conventional animals" by Beaver and Wostmann.
1965
"Molecules as documents of evolutionary history" by Emile Zuckerkandl and Linus Pauling.
A must-read for everyone interested in studying molecular evolution.
"Indigenous, normal, and autochthonous flora of the gastrointestinal tract" by Dubos and colleagues.
In this paper, the authors said the following:
"Animals and human beings have evolved in intimate and constant association with a complex microflora and microfauna. Under natural conditions, the development and functions of their tissues are influenced by countless microorganisms which are always present in the digestive and respiratory tracts, and probably also in other organs. It is to be expected, therefore, that anatomical structures and physiological needs have been determined in part of the microbiota which prevailed during evolutionary development, and that many manifestations of the body at any given are influenced by the microbiota now present. It can be taken for granted, in other words, that the microbiota is part of the environment to which animals and man have had to become adapted, and on which they have come to depend".
Also, "Many facts, not to be described here, have revealed that the indigenous microbiota can influence the morphological and physiological characteristics of its host to such an extent that traits assumed to be the unavoidable consequences of the genetic endowment are determined in reality by the microbial environment."
One can only wonder how many scientists in our times have missed such important thoughts in their work.
"Probiotics: growth-promoting factors produced by microorganisms" by Lilly and Stillwell.
1966
"Gases produced by human intestinal microflora" by Calloway et al.
1967
"On the origin of mitosing cells" by Lynn Sagan.
1968
"Relationship between cell size and time of initiation of DNA replication" by Donachie.
1971
"Changes in the microflora of man during long-term confinement" by Shilov et al.
1972
"Introduction to intestinal microecology" by T.D. Luckey.
In this paper, the author mentioned that "life is possible without germs" and that "germfree mice live twice as long as classic mice".
1973
"The relationshp between the host and its intestinal microflora" by Schaedler.
1974
"Space microbiology" by Gerald R. Taylor.
1976
"Nutritional determinants of the ecology of the oral flora" by Morhart and Fitzgerald.
1978
"Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli" by Brosius et al.
In the last paragraph of this paper, the authors presented an interesting discussion about the possible coding functions of 16S rRNA, without, rather unfortunately, providing any useful reference.
1979
"Tropical sprue: a review" by O´Brien.
If someone wonders about why including something like in this library, see this paper.
"Environmental contaminants and intestinal function" by Banwell.
"Bacterial bioluminescence: its control and ecological significance" by Nealson and Hastings.
"Intestinal microbial flora of the of the American cockroach, Periplaneta americana L." by Bracke et al.
1980
"The microbial contribution to human faecal mass" by Stephen and Cummings.
1982
"Structure and evolution of ribosomes" by H.G. Wittmann.
This work represents a great overview about ribosomes. For instance, there is a very interesting section about the architecture of the ribosome.
"Inhibition and control of bacterial spore germination" by Smoot and Pierson.
1983
"Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids" by Woese and colleagues.
The purpose of the review was "to bring up-to-date and discuss in detail the status of 16S rRNA secondary structure and to present an overview on this rapidly developing field". Incredibly amazing.
"The use of a human donor flora for recontamination following antibiotic decontamination" by Heidt and colleagues.
This early paper may be of interest for those interested in Fecal Microbiota Transplantation.
1984
"Gastrointestinal microecology in the critically ill neonate" by Bell et al.
In this paper, yeast retrival was increased in the feces of the ill neonates.
"Microbial aspects of the cockroach hindgut" by Cruden and Markovetz.
Interestingly, the authors noted that the hindgut of Euderces posticus was highly methanogenic.
"Bacterial transmigration as an indicator of time of death" by Melvin et al.
"The respiratory chains of Escherichia coli" by Ingledew and Poole.
"Shrinkage of growing Escherichia coli cells by osmotic challenge" by Koch.
1986
"Microbial ecology and evolution" by Olsen et al.
One of the very best reviews on the topic, coauthored by Norman R. Pace.
1987
"Bacterial evolution" by Carl R. Woese.
1988
"Evolutionary relationships among cyanobacteria and green chloroplasts" by Giovannoni et al.
"The ribosomal gene spacer region in archaebacteria" by Achenbach-Richter and Woese.
1989
"A brief note concerning archaebacterial phylogeny" by Olsen and Woese.
"Probiotics in man and animals" by Fuller.
A classic indeed.
"Fibre, Fermentation, Flora, and Flatus" by Grimble.
1990
"Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya" by Carl R. Woese, Otto Kandler and Mark L. Wheelis.
In this fascinating paper, the authors mention that "one structural feature in the small subunit rRNA by which the eubacteria can be distinguished from archaebacteria and eukaryotes is the hairpin loop lying between positions 500 and 545" based on this paper.
"High diversity in DNA of soil Bacteria" by Torsvik et al.
"Our results indicate that the diversity of the total bacterial community in a deciduous-forest soil is so high that diversity indices based on DNA heterogeneity can be determined only with difficulty".
"Probiotics in animal nutrition: a review" by Vanbelle et al.
First sentence of the abstract: "The normal microflora colonizing the digestive tract in livestock species at five to six days after birth can be summarized as following: 400 to 500 different bacterial strains for a total count of 10(14) bacteriae".
1992
"How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity" by Fox et al.
Despite focusing only on a few members of Bacillus, this paper highlights the drawback of using 16S rRNA gene to catalogue organisms into "species".
1994
"There must be a prokaryote somewhere: microbiology's search for itself" by Carl E. Woese.
1995
"Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics" by Gibson and Roberfroid.
In this paper, the authors said that "Indeed, the data of Bouhnik et al. (1992) indicate that when the product containing the probiotic is not longer consumed, the added bacteria are rapidly washed out of the colon"
1996
"Human colonic biota studied by ribosomal DNA sequence analysis" by Wilson and Blitchington.
One of the first studies using 16S clone libraries to study the human gut microbiota.
"Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora" by Miller and Wolin.
1997
"Intestinal flora and endogenous vitamin synthesis" by Hill MJ.
Ever since I can remember I have had a hard time finding good references for microbial synthesis of vitamins. I have not read this paper and the abstract does not give much details but here you go! In this regard, you may also be interested in reading Fang's paper from 2017 below.
"Effects of short-chain fatty acids on the inflamed colonic mucosa" by Scheppach et al.
An excellent early overview of the relationship between butyrate and other short-chain fatty acids (SCFAs) and colonocytes' health. Importantly, SCFAs are produced by a variety of gut microbes such as Clostridium, Eubacterium, Butyrivibrio and others. Lots of papers have been published about this important topic. In particular, Donohoe et al. (2011) showed that "when butyrate is added to germfree colonocytes, it rescues their deficit in mitochondrial respiration and prevents them from undergoing autophagy. The mechanism is due to butyrate acting as an energy source rather than as an histone deacetylase (HDAC) inhibitor".
"The intestinal microflora during the first weeks of life" by Eugenia Bezirtzoglou.
1998
"Two empires or three?" by Ernst Mayr.
"Transcription and translation in Archaea: a mosaic of eukaryal and bacterial features" by Bell and Jackson.
"The universal ancestor" by Carl Woese.
"Propagation by sporulation in the guinea pig symbiont Metabacterium polyspora" by Angert and Losick.
"Ecological control of the gastrointestinal tract. The role of probiotic flora" by Bengmark.
"How Did Bacteria Come to Be?" by Arthur L. Coch.
"The intestinal ecosystem in chronic functional constipation" by Zoppi et al.
"Use of 16S rDNA community fingerprints to study cricket hindgut microbial communities" by Santo Domingo.
1999
"An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria" by Asai et al.
"The results suggest that, contrary to common belief, coevolution of rRNA with many other components in the translational machinery may not completely preclude the horizontal transfer of rRNA genes".
"Haloarcula quadrata sp. nov., a square, motile archaeon isolated from a brine pool in Sinai (Egypt)" by Oren et al.
This group of Archaeas are predominantly squared-shaped.
"Calibrating bacterial evolution" by Ochman et al.
"Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut" by Suau et al.
One of the first studies using 16S clone libraries to study the human gut microbiota.
2000
"Shared and unique environmental factors determine the ecology of methanogens in humans and rats" by Florin et al.
"Bifidobacterium strains from resident infant human gastrointestinal microflora exert antimicrobial activity" by Lievin et al.
"How quantitative is quantitative PCR with respect to cell counts?" by Ludwig and Schleifer.
2001
"Fate and dissemination of Bacillus subtilis spores in a murine model" by Tran Thu Hoa et al.
Very interesting, in the abstract the authors said that: "However, we found that the number of spores excreted in the feces of mice was, in some experiments, larger than the original inoculum. This was an intriguing result and might be explained by germination of a proportion of the spore inoculum in the intestinal tract, followed by limited rounds of cell growth and then sporulation again. This result raises the interesting question of whether it is the spore or the germinated spore that contributes to the probiotic effect of bacterial spores".
"Quorum sensing in bacteria" by Miller and Bassler.
2002
"New technologies, human-microbe interactions, and the search for previously unrecognized pathogens" first paper in PubMed with the word "microbiome"
"The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification" by Cavalier-Smith.
"Development of 16S rRNA-gene-targeted group-specific primers for the detections and identification of predominant bacteria in human feces" by Matsuki et al.
"What are bacterial species?" by Cohan.
2003
"Pathogenic archaea: do they exist?" by Cavicchioli et al.
"Archaea and their potential role in human disease" by Eckburg et al.
2004
"Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies" by Jaspers and Overmann.
Thinking that similar 16S rRNA gene sequences comes from similar microorganisms? Think it twice.
"Evolution of bacterial diversity and the origins of modularity" by Rainey and Cooper.
This paper is not only extremely entretaining and useful for microbial ecologists but it can also open new venues of research within this field. Other cool stuff can be found in the Rainey Lab.
2005
"The interaction between bacteria and bile" by Begley et al.
"Host-bacterial mutualism in the human intestine" by Bäckhed et al.
"Diversity of the human intestinal microbial flora" by Eckburg.
This paper is interesting for various reasons, but it is indeed impressive that in 2005 a paper in Science refers to the microbiota as "microbial flora".
"The use of bacterial spore formers as probiotics" by Hong et al.
"Understanding the nature of this probiotic effect is complicated, not only because of the complexities of understanding the microbial interactions that occur within the gastrointestinal tract, but also because Bacillus species are considered allochthonous microorganisms"
"Defining the normal bacterial flora of the oral cavity" by Aas et al.
"Opinion: Re-evaluating prokaryotic species" by Gevers et al.
"Bacterial concepts in irritable bowel syndrome" by Lin and Pimentel.
2006
"Open software for biologists: from famine to feast" by Field et al.
An interesting commentary about community empowerment and democratizing access to computing environments and expertise.
"Phenotypic variation in bacteria: the role of feedback regulation" by Smits et al.
"The selective value of bacterial shape" by Kevin D. Young.
Amazing review on a fascinating topic.
"Ecological and evolutionary forces shaping microbial diversity in the human intestine" by Ley et al.
"The bacterial species dilemma and the genomic–phylogenetic species concept" by James T. Staley.
A marvelous account of a formidable topic.
"Microbial cell individuality and the underlying sources of heterogeneity" by Avery.
"Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection" by van der Sluis et al.
This paper is particularly interesting in a context of Akkermansia and other mucus degraders.
"The intestinal life cycle of Bacillus subtilis and close relatives" by Tam et al.
"Introduction: how and when did microbes change the world?" by Cavalier-Smith et al.
"Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study" by Mueller et al.
2007
"Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities" by Lozupone et al.
This paper is very useful for introducing the weighted UniFrac but also because it contains a -short- explanation between PCA and PCoA. I also found this with comprehensible explanations for both.
"Yeast forms dominate fungal diversity in the deep oceans" by David Bass et al.
"Size doesn't matter: towards a more inclusive philosophy of Biology" by O´Malley and Dupré.
The authors suggest "that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity."
"The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains" by Becerra et al.
"Metabolic syndrome in insects triggered by gut microbes" by Schilder and Marden.
"The Plate Debate: Cultivable communities have no utility in contemporary environmental microbial ecology" by Karl Ritz.
"Probiotics: 100 years (1907-2007) after Elie Metchnikoff’s observation" by Anukam et al.
2008
"Human gut microbiota and bifidobacteria: from composition to functionality" by Turroni et al.
"Active Crohn’s disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora" by Swidsinski et al.
In this paper, the authors said: "the homogenization of feces obscures the results, making the correct evaluation of the microbial community impossible".
"Resistance, resilience, and redundancy in microbial communities" by Allison and Martiny.
"Individuality in Bacteria" by Carla J. Davidson and Michael G. Surette.
"The organization of the bacterial genome" by Eduardo Rocha.
"Ecology and genomics of Bacillus subtilis" by Earl et al.
"Germination and outgrowth of Bacillus subtilis and Bacillus licheniformis spores in the gastrointestinal tract of pigs" by Leser et al.
"Safety assessment of dairy microorganisms: The Enterococcus genus" by Ogier y Serror.
"The social behaviours of bacterial pathogens" by Popat et al.
2009
"On the origin of prokaryotic species" by W. Ford Doolittle and Olga Zhaxybayeva.
Have you ever wondered why we talk about "species" (i.e. group of organisms capable of producing fertile descendants) when referring to microorganisms? If you are doing any research on microorganisms this can be of great interest to you.
"The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework" by Rosenberg et al.
This paper is interesting for many reasons, but it is particularly exciting for me because the theory of inheritance of acquired characteristics developed by Lamarck and others before him was long considered to be erroneous.
"Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria" by Kuo and Ochman.
"Screening of yeast strains for phytase activity" by Olstorpe et al. This paper is interesting in a context of rickets and yeast supplementation (see papers above from the 1940's).
"Bacillus subtilis isolated from the human gastrointestinal tract" by Hong et al.
"As part of an ongoing study to determine the true habitat of Bacillus species......" What a way to start an abstract.
"Shifting the genomic gold standard for the prokaryotic species definition" by Richter and Rosello Mora.
"Bacterial competition: surviving and thriving in the microbial jungle" by Hibbing et al.
2010
"Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm" by Jens Walter et al.
An excellent paper that talks about the evolutionary processes that have shaped symbiotic interactions in the vertebrate gut. Also, please note that some colleagues hold the belief that probiotics are more likely to be effective if they originate from the same host to which they ought to be administered. In this regard, the authors said that: "It is a logical working hypothesis that symbionts that share an evolutionary fate with their host are more likely to possess adaptive traits that provide benefits".
"Origin and evolution of the ribosome" by George E. Fox.
While a lot of research has been done on ribosomes, this paper offers a unique trip into this amazing subject.
Has the microbiota played a critical role in the evolution of the adaptive immune system? by Lee and Mazmanian.
When referring to the microbial communities that inhabit our bodies, the authors say that "These polymicrobial communities contribute profoundly to the architecture and function of the tissues they inhabit, and thus play an important role in the balance between health and disease".
"The evolutionary aspects of aquaporin family" by Ishibashi et al.
"Human intestinal spirochetosis – a review" by Tsinganou and Gebbers.
Many of us in the biomedical field learned in school about Leptospira and its relationship with kidney disease. However, Leptospira is much more than that.
"Guidance for Substantiating the Evidence for Beneficial Effects of Probiotics: Prevention and Management of Infections by Probiotics" by Wolvers et al.
"Microbiology and the species problem" by Ereshefsky.
"Effects of four Bifidobacteria on obesity in high-fat diet induced rats" by Yin et al.
The authors say here that "Different strains of Bifidobacteria might drive different directions of fat distribution.".
2011
"Towards an evolutionary model of animal-associated microbiomes" by Yeoman et al.
A fascinating deep trip into the reasons/characteristics behind close associations between animals and their microbiomes.
"Interaction between obesity and the gut microbiota: relevance in nutrition" by Delzenne and Cani.
Ley et al. in 2005 showed that compared with lean mice, obese animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes, thus leading to a higher Firmicutes/Bacteroidetes ratio. While this phenomenon has been confirmed in other studies, this is not a universal phenomenon at all and Delzenne and Cani made a wonderful job at reviewing this topic enjoy!
"A study in balance: How microbiomes are changing the shape of environmental health" by Kellyn S. Betts.
As Silbergeld puts it: “We may exist at the pleasure of the microbes”
"Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans" by Muegge et al.
In this paper, the authors reasoned "that if bacterial taxa or functions originated rarely, then these taxa or functions should be vertically transmitted during mammalian speciation. Therefore, there should be more cases in which a given taxon or function occurred in all members of a monophyletic mammalian group than chance would predict".
"Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve" by Bravo et al.
"Characterization of the diversity and temporal stability of bacterial communities in human milk" by Hunt et al.
"Normal gut microbiota modulates brain development and behavior" by Diaz Heijtz et al.
"Enterotypes of the human gut microbiome" by Arumugan et al.
Introduction to the idea of "enterotypes".
"Linking long-term dietary patterns with gut microbial enterotypes" by Wu et al.
"Health benefits of probiotics: are mixtures more effective than single strains?" by Chapman et al.
"A review of molecular methods to study the microbiota of soil and the mycosphere" by van Elsas and Boersma.
"Supervised classification of human microbiota" by Knights et al.
"Salmonella spp. survival strategies within the host gastrointestinal tract" by Alvarez-Ordoñez et al.
"Bacterial biogeography of the human digestive tract" by Stearns et al.
2012
"Beyond the Venn diagram: the hunt for a core microbiome" by Shade and Handelsman.
Much has been said in the literature about the "core" microbiome but this paper reviews all of it very nicely. The authors also mention that "Many multivariate analyses for exploring microbial communities (multidimensional scaling or distance-based analyses) weigh more abundant OTUs more heavily, resulting in patterns driven by the most abundant OTUs". I experienced this myself in the wheat paper (PeerJ 2016) but I would like to dig a bit more in it.
"Human gut microbiome viewed across age and geography" by Yatsunenko et al.
"Quorum sensing in fungi – a review" by Albuquerque and Casadevall.
Quorum sensing (QS) is a fascinating phenomenon that has been deeply studied in bacteria. QS in eukaryotic organisms was unknown until the discovery in 2001 of farnesol as a QS molecule in the pathogenic fungus Candida albicans (2001 paper). This paper provides an excellent overview of QS in fungi.
"Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life" by Norman R. Pace et al.
"High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity" by Loman et al.
"Systematic review of randomized controlled trials of probiotics, prebiotics, and synbiotics in inflammatory bowel disease" by Ghouri et al.
"To date, there is insufficient data to recommend probiotics for use in CD."
"A Symbiotic View of Life: We Have Never Been Individuals" by Gilbert et al.
"Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome" by Bhullar et al.
"Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon" by Ze et al.
"From the regulation of peptidoglycan synthesis to bacterial growth and morphology" by Typas et al.
"Diversity and distribution of sulphate-reducing bacteria in human faeces from healthy subjects and patients with inflammatory bowel disease" by Jia et al.
"Competition, not cooperation, dominates interactions among culturable microbial species" by Foster and Bell.
2013
"The gut microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity" by Hermann-Bank et al.
Interesting approach, I wonder if you could also combine it with other sequencing platforms (Illumina, ION Torrent, etc.)
"Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units" by Koeppel and Wu.
OTUs frequently spanned multiple ecological habitats. They demonstrate that ecological heterogeneity is caused by their phylogenetic inconsistency. Fascinating paper!
"Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names" by Yarza et al.
"The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition" by Hyde et al.
Very few papers have studied the fascinating process of microbial decomposition.
"New Insights from Existing Sequence Data: Generating Breakthroughs without a Pipette" by Plocik and Graveley.
Although archived sequence data is getting bigger and faster than anyone could have anticipated, very few papers discuss the re-use of this archived data for new discoveries for the benefit of science.
"Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status" by William G. Branton et al.
"Mom knows best: the universality of maternal microbial transmission" by Funkhouser and Bordenstein.
An excellent review of a fascinating topic.
"The biology of habitat dominance; can microbes behave as weeds?" by Cray et al.
"Robust estimation of microbial diversity in theory and in practice" by Haegeman et al.
"The effects of model choice and mitigating bias on the ribosomal tree of life" by Lasek-Nesselquist and Gogarten.
"The gut microbiota--masters of host development and physiology" by Sommer and Backhed.
"Bacteria as vitamin suppliers to their host: a gut microbiota perspective" by LeBlanc et al.
"The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses" by Větrovský and Baldrian.
2014
"The placenta harbors a unique microbiome" by Kjersti Aagaard et al.
This paper received an interesting comment from Harvey J. Kliman from Yale University School of Medicine. As a service to the community, Science has made this comment (and its corresponding Response from the authors) free to the community. Just create an account in their website to get these documents. In his blog "The Tree of Life", Jonathan Eisen from UC Davis wrote a couple of very interesting comments about this (http://phylogenomics.blogspot.mx/2014/05/overselling-microbiome-award-many-for.html).
Thanks to Zach T. Lewis, I became aware of yet another paper showing that the placental "microbiome" could not be distinguished from contamination introduced during DNA purification (http://www.ncbi.nlm.nih.gov/pubmed/27338728)
And thanks to an anonymous reviewer of a recent paper from our team, I also found this other paper that refutes the possibility that the placenta harbors a microbiome, at least in ruminants.
Here is another recent comment by Nicola Segata about this.
"The Earth Microbiome project: successes and aspirations" by Jack A Gilbert, Janet K Jansson and Rob Knight.
I love the final comment in this paper: "As we move forward, we will continue to explore new avenues for collaboration, including potentially going beyond the Earth to explore extra-terrestrial locations".
"Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences" by Jai Ram Rideout et al.
There are different ways to assign your sequences to Operational Taxonomic Units. For example, the QIIME script pick_closed_reference_otus.py try to match your sequences to a reference database (for example the GreenGenes 16S reference database). If the input sequence does not match any reference sequence at a user-defined percent identity threshold (say 97%), that sequence is excluded. This is VERY PROBLEMATIC for several reasons, especially in environments with few representatives in databases. In this paper, Jai and collaborators published an excellent alternative for OTU picking. I expect many researchers would start using and citing this publication. In my short experience using it, researchers can detect many more OTUs compared to closed_reference methods.
"The treatment-naïve microbiome in new-onset Crohn’s disease" by Gevers et al.
In this paper describe a microbial dysbiosis index, which helped create a QIIME script that computes this index. This is very interesting because the term dysbiosis is very difficult to understand due to the millions of microorganisms inhabiting the gut. The idea of a microbial dysbiosis index has also been discussed in small animal medicine by my advisor Jan Suchodolski (link to the paper).
"Bacteria from diverse habitats colonize and compete in the mouse gut" by Seedorf et al.
This is one of the most interesting studies there are. If one observes the presence of bacteria, let's say in soil, one may conclude that the bacteria are specialized in that particular environment; therefore one could say that it is very unlikely that bacteria from one environment can thrive in another environment. Well, this paper shows otherwise.
"Life in a world without microbes" by Gilbert and Neufeld.
An excellent discussion of a super exciting topic.
"Conducting a Microbiome Study" by Goodrich et al.
"From microbe to man: the role of microbial short chain fatty acids metabolites in host cell biology" by Natarajan and Pluznick.
"Geographical variation of human gut microbial composition" by Suzuki and Worobey.
"Diet rapidly and reproducibly alters the human gut microbiome" by David et al.
"Germination of spores of Bacillus species: what we know and do not know" by Peter Setlow.
"Bacterial influences on animal origins" by Alegado and King.
"Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible" by McMurdie and Holmes.
"Diet and the development of the human intestinal microbiome" by Voreades et al.
"The mycobiota: interactions between commensal fungi and the host immune system" by Underhill and Iliev.
"Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes" by Kim et al.
"New insights into the hygiene hypothesis in allergic diseases" by Penders et al.
"The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types" by Lang et al.
"Helicobacter pylori: Friend or foe?" by Malnick et al.
2015
"Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD" by Casén et al.
"Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity" by He et al.
An excellent addition to the literature about the stability of OTUs, a poorly discussed topic in the field of microbial ecology.
"An introduction to recurrent nucleotide interactions in RNA" by Sweeney et al.
An excellent introduction to nucleotide interaction in RNA secondary structures.
"Methanogen communities in stools of humans of different age and health status and co-occurrence with bacteria" by Vanderhaeghen et al.
Methanogenesis is an ancient metabolic process and it is very interesting that these microorganisms inhabit the human and animal gut microbiota.
"The ecology of the microbiome: Networks, competition, and stability" by Coyte et al.
Interestingly, independently developed models converged on a surprising answer: A high diversity of species is likely to coexist stably when the system is dominated by competitive, rather than cooperative, interactions.
"The dormant blood microbiome in chronic, inflammatory diseases" by Potgieter et al.
Yes, there is a complex microbiome in our blood.
"Diverse uncultivated ultra-small bacterial cells in groundwater" by Luef et al.
Figure 4 of this paper is truly amazing, these bacteria belong to something called dark microbial matter and are truly very small, about 0.009 cubic microns. They have tightly packed spirals (inferred to be DNA), few densely packed ribosomes and a variety of pili-like structures that might enable inter-organism interactions.
"Microbial taxonomy in the post‑genomic era: Rebuilding from scratch?" by Thompson et al.
An excellent contribution about a very important (yet often neglected) topic in microbiology.
"Impermanence of bacterial clones" by Bobay et al.
"The non-biological meaning of the term "prokaryote" and its implications" by Di Giulio.
"Small but Mighty: Cell Size and Bacteria" by Levin and Angert.
"The ribosome as a missing link in the evolution of life" by Meredith and Robert Root-Bernstein.
"The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’" by Nick Lane.
"Social networks predict gut microbiome composition in wild baboons" by Tung et al.
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. The authors showed that rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship, and shared environments.
"A ribosome without RNA" by Bernhardt and Tate.
"Host immunostimulation and substrate utilization of the gut symbiont Akkermansia muciniphila" by Noora A. Ottman. PhD Thesis, Wageningen University.
"Saccharomyces cerevisiae: a nomadic yeast with no niche?" by Goddard and Greig.
"The microbiome of the urinary tract—a role beyond infection" by Whiteside et al.
"The Characterization of Feces and Urine: A Review of the Literature to Inform Advanced Treatment Technology" by Rose et al.
Very interesting:
"Fecal wet mass values were increased by a factor of 2 in low income countries (high fiber intakes) in comparison to values found in high income countries (low fiber intakes). Feces had a median pH of 6.64 and were composed of 74.6% water. Bacterial biomass is the major component (25–54% of dry solids) of the organic fraction of the feces. Undigested carbohydrate, fiber, protein, and fat comprise the remainder and the amounts depend on diet and diarrhea prevalence in the population. The inorganic component of the feces is primarily undigested dietary elements that also depend on dietary supply".
"Control of brain development, function, and behavior by the microbiome" by Sampson and Mazmanian.
"Temporal patterns of rarity provide a more complete view of microbial diversity" by Shade and Gilbert.
"Insights from 20 years of bacterial genome sequencing" by Land et al.
"Analysis of composition of microbiomes: a novel method for studying microbial composition" by Mandal et al.
"Bifidobacterium longum subspecies infantis: champion colonizer of the infant gut" by Underwood et al.
"Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa" by Trosvik and de Muinck.
2016
"A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling" by D'Amore et al.
This is a very useful paper but "running a small trial consisting of several hypervariable regions to quantify the discriminatory power of each region" may not feasible for all researchers and may actually complicate things further (for instance, how exactly can someone objectively decide which region is better than others?)
"De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units" by Westcott and Schloss.
This paper "call into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME". Holy molly.
"Dysbiosis is not an answer" by Olesen and Alm.
"Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals" by Ormerod et al.
There are many so called uncultured members in the gut, soil etc microbiota that challenge our understanding of these important microbial ecosystems. This paper analyzed the genomes of several members of the group S24-7 (within the Bacteroidales) thus shedding light into an important and abundant member of the gut microbiota.
"Microbiota-mitochondria inter-talk: consequence for microbiota-host interaction" by Saint-Georges-Chaumet and Edeas.
This is the first time (I think) that I read about a possible relationship between the mitochondria of host cells and the microbiota.
"Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments" by Desiree C Yang et al.
"The physiology and habitat of the last universal common ancestor" by Weiss et al.
I have no words, the paper is simply worth reading.
"Do microbiotas warm their hosts?" by Rosenberg and Zilber-Rosenberg.
Very interesting: We estimate that microbial metabolism in the human gut, for example, produces 61 kcal/h, which corresponds to approximately 70% of the total heat production of an average person at rest.
"The bright side of microbial dark matter: lessons learned from the uncultivated majority".
In this paper, the authors discuss the so called dark microbial matter, which have opened up a new world into microbial cooperation and dependence.
"Psychobiotics and the Manipulation of Bacteria−Gut−Brain Signals" by Amar Sakar et al.
First time I hear about this interesting term.
"Revised Estimates for the Number of Human and Bacteria Cells in the Body" by Render et al.
"Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle" by Gorvitovskaia et al.
A very interesting article proposing that "previous findings citing Bacteroides- and Prevotella-dominated clusters are the result of an artifact caused by the greater relative abundance of these two taxa over other taxa in the human gut and the sparsity of Prevotella abundant samples".
"Revised estimates for the number of human and Bacteria cells in the body" by Sender et al.
"Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota" by Lauder et al.
"Low abundant soil bacteria can be metabolically versatile and fast growing" by Kurm et al.
The thoughts in this paper are useful for other microbial environments.
"Expanding the UniFrac toolbox" by Wong et al.
"Centenary of the death of Elie Metchnikoff: a visionary and an outstanding team leader" by Cavaillon and Legout.
"Effect of probiotics on central nervous system functions in animals and humans: a systematic review" by Wang et al.
"Transcriptional interactions suggest niche segregation among microorganisms in the human gut" by Plichta et al.
"Bifidobacteria and their role as member of the human gut microbiota" by O'Callaghan and van Sinderen.
"A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility" by Desai et al.
"Vertebrate bacterial gut diversity: size also matters" by Godon et al.
"Population-level analysis of gut microbiome variation" by Falony et al.
In this paper, the authors suggest that stool consistency is the most influential factor affecting the microbiome community variation.
"Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies" by Se Jin Song et al.
As in other studies, we strongly caution against the use of 70% ethanol.
"Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation" by Browne et al.
"Cross-species comparisons of host genetic associations with the microbiome" by Goodrich et al.
"The effect of host genetics on the gut microbiome" by Bonder et al.
2017
"The prenatal gut microbiome: Are we colonized with bacteria in utero?" by Walker et al.
This paper contains a very nice picture about the maternal sites that may contribute to offspring gut microbiome.
"Heart failure is associated with depletion of core intestinal microbiota" by Luedde et al.
I am not sure how one thing relates to the other but I think is definitely something worth to look at.
"The fecal microbiome of ALS patients" by Brenner et al.
First time I hear about Amyotrophic lateral sclerosis. There was absolutely no difference in fecal microbiota between patients with ALS and healthy patients, using 16S sequencing and PICRUSt.
"Asgard archaea illuminate the origin of eukaryotic cellular complexity" by Zaremba-Niedzwiedzka et al.
In this paper the authors say that "Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell"
"An Important Role for Purifying Selection in Archaeal Genome Evolution" by Lyu et al.
"We found that bigger bacterial genomes indeed experienced stronger purifying selection, but the opposite was observed in archaeal genomes".
"Comprehensive evaluation of the bactericidal activities of free bile acids in the large intestine of humans and rodents" by Watanabe et al.
I simply did not know that some bile acids exhibit antimicrobial activity.
I have always been interested in the statistical analysis of microbial communities and the current literature is often confusing, at least for me (e.g. there are many different methods). Just recently, Rob Knight and colleagues published a very useful paper about this with emphasis on False Discovery Rate.
"Exact sequence variants should replace operational taxonomic units in marker-gene data analysis" by Callahan et al.
Yes, seriously. This paper deals with a possible replacemente of OTUs.
"Multiple approaches detect the presence of fungi in human breastmilk samples from healthy mothers" by Boix-Amoros et al.
"Critical Issues in Mycobiota Analysis" by Halwachs et al.
In here I learned about the so called species hypotheses.
"Exploring the under-investigated “microbial dark matter” of drinking water treatment plants" by Bruno et al.
I have heard the term "microbial dark matter" before but this paper discusses this topic elegantly. Actually, I found lots of other very interesting papers about this topic (just search for the word "dark" in this page).
"Microbiome: Puppy power" by Sujata Gupta.
Excellent article about a topic of uttermost importance. In this article, the author said that "Babies who share their homes with a dog are much less likely to grow up into adults with allergies than those who don't".
"Microbial production of vitamin B12: a review and future perspectives" by Fang et al.
"Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life" by Spang et al.
"Evolutionary biology needs wild microbiomes" by Sarah M. Hird.
The section of "Field collection of wild microbiomes" may be of particular interest for some researchers.
"A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome" by Perez-Muñoz et al.
"Hair growth in two alopecia patients after Fecal Microbiota Transplant" by Rebello et al.
"Dysbiosis and its discontents" by Hooks and O´Malley.
"Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis" by Pammi et al.
"A review of dose-responses of probiotics in human studies" by Ouwehand.
"Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life" by Larsen et al.
"Our estimates suggest that there are likely to be at least 1 to 6 billion species on Earth. Furthermore, in contrast to previous estimates, the new Pie of Life is dominated by bacteria (approximately 70–90% of species) and insects are only one of many hyperdiverse groups"
"Temporal dynamics of the gut microbiota in people sharing a confined environment, a 520-day ground-based space simulation, MARS500" by Turroni et al.
"Balance Trees Reveal Microbial Niche Differentiation" by Morton et al.
This paper refers to gneiss.
"The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota" by Milani et al.
"The gut microbiota as a modulator of innate immunity during melioidosis" by Lankelma et al.
"Oscillospira and related bacteria - From metagenomic species to metabolic features" by Gophna et al.
2018
"Mouse models for human intestinal microbiota research: a critical evaluation" by Hugenholtz and de Vos.
A lot of the information we have about the gut microbiota comes from mouse models, yet these models may or may not truly reflects the human microbiota.
"Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium" by Tapiainen et al.
Is this evidence of a microbial preload before birth?
"Costs and benefits of provocation in bacterial warfare" by Gonzalez et al.
"Fallopian tube microbiota: evidence beyond DNA" by Pelzer et al.
"In the absence of inflammatory pathology, the fallopian tube harbors a visually observable microbial population, which correlates with cultivation-dependent and -independent data, further refuting the sterility of this anatomical niche." Very interesting.
"An expanded genomic representation of the phylum Cyanobacteria" by Soo et al.
"Our findings are consistent with theories that photosynthesis occurred late in the Cyanobacteria and involved extensive lateral gene transfer and extends the recognized functionality of members of this phylum".
"Cancer cells arise from bacteria" by Dong and Xing.
Very interesting proposal.
"Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole" by Osmanovic et al.
"Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How?" by Geerlings et al.
A fascinating review on a fascinating topic.
"Extensive impact of non-antibiotic drugs on human gut bacteria" by Maier et al.
"Bifidobacteria and the infant gut: an example of co-evolution and natural selection" by Turroni et al.
"The gut-liver axis and the intersection with the microbiome" by Tripathi et al.
"Rhizosphere microorganisms can influence the timing of plant flowering" by Lu et al.
"Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations" by Eisenhofer et al.
"Low Diversity Gut Microbiota Dysbiosis: Drivers, Functional Implications and Recovery" by Kriss et al.
"Analysis and correction of compositional bias in sparse sequencing count data" by Senthil Kumar et al.
"Resuscitation of anammox bacteria after >10,000 years of dormancy" by Zhu et al.
"Functions of the Microbiota for the Physiology of Animal Metaorganisms" by Esser et al.
"The distribution of bacterial doubling times in the wild" by Gibson et al.
"Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions" by Chelakkot et al.
"Keystone taxa as drivers of microbiome structure and functioning" by Banerjee et al.
2019
"The super-donor phenomenon in fecal microbiota transplantation" by Wilson et al.
"Extensive transmission of microbes along the gastrointestinal tract" by Schmidt et al.
The authors say that "by studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals".
"Multi-method characterization of the human circulating microbiome" by Whittle et al.
The so called "blood microbiome" is a very exciting yet relatively unexplored topic.
"Gut microbiota density influences host physiology and is shaped by host and microbial factors" by Contijoch et al.
First time I read something about the density of the gut microbiota.
"Bacteriophages of the human gut: the ‘‘known unknown’’ of the microbiome" by Shkoporov and Hill.
"Probiotics: if it does not help it does not do any harm. Really?" by Lerner et al.
"Not all animals need a microbiome" by Hammer et al.
"The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth" by Stinson et al.
"Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host" by Lavelle et al.
This paper is important for various reasons but more importantly because each individual is different and the role of the baseline gut microbiota.
"An apple a day: which Bacteria do we eat with organic and conventional apples?" by Wassermann et al.
"Our results suggest that we consume about 100 million bacterial cells with one apple".
"Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean" by Pereira et al.
"Problems with the concept of gut microbiota dysbiosis" by Harald Brüssow.
"Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant" by De Filipp et al.
"Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals" by Vuik et al.
"High-starch diets alter equine faecal microbiota and increase behavioural reactivity" by Bulmer et al.
"Filling the gap between collection, transport and storage of the human gut microbiota" by Martinez et al.
In this paper, there are very interesting results about the effect of GutAlive in the presence of Bifidobacterium bifidum and Faecalibacterium prausnitzii.
"Rarefaction, Alpha Diversity, and Statistics" by Amy D. Willis.
"Phage tail-like particles are versatile bacterial nanomachines – A mini-review" by Patz et al.
"Multiple levels of the unknown in microbiome research" by Thomas and Segata.
"Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut" by Fung et al.
"Microbial evolution and ecological opportunity in the gut environment" by Pauline D. Scanlan.
"Impact of Physical Exercise on Gut Microbiome, Inflammation, and the Pathobiology of Metabolic Disorders" by Sohail et al.
"Role of the Gut Microbiome in Autism Spectrum Disorders" by Pulikkan et al.
"Gastrointestinal problems that are seen associated with most of the autism cases suggest that it is not just a psychiatric disorder as many claim but have a physiological base, and alleviating the gastrointestinal problems could help alleviating the symptoms by bringing out the much needed overall improvement in the affected victims."
"Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study" by Depommier et al.
In this study, the authors administered 1x1010 bacteria (either alive or pasteurized) daily for 3 months, with the specific advice to keep their normal dietary intake and physical activity during the study period.
"Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut" by Fung et al.
"Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research" by Hooks and O'Malley.
2020
"Risk factors that predict the failure of multiple fecal microbiota transplantations for Clostridioides difficile infection" by Allegretti et al.
"Long-term effects of antimicrobial drugs on the composition of the human gut microbiota" by Mulder et al.
"Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study" by Clooney et al.
"Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome are mirrored by changes in gut microbiome" by Goll et al.
"Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease" by Ghosh et al.
"A complete domain-to-species taxonomy for Bacteria and Archaea" by Parks et al.
"Analysis of compositions of microbiomes with bias correction" by Lin and Das Peddada.
"On a Non-Discrete Concept of Prokaryotic Species" by Gonzalez et al.
"Does diversity beget diversity in microbiomes?" by Madi et al.
"Deep microbial community profiling along the fermentation process of pulque, a biocultural resource of Mexico" by Rocha-Arriaga et al.
"Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals" by Vaga et al.
"Increasing Evidence That Irritable Bowel Syndrome and Functional Gastrointestinal Disorders Have a Microbial Pathogenesis" by Carco et al.
2021
"Large-scale association analyses identify host factors influencing human gut microbiome composition" by Kurilshikov et al.
"Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon" by Tarracchini et al.
"Role of gut microbiota in functional constipation" by Zhang et al.
"The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics" by Salminen et al.
"Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment" by Marcos-Zambrano et al.
"Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay" by Tudela et al.
"Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters" by Patrick D. Schloss.
2022
"Long-term diosmectite use does not alter the gut microbiota in adults with chronic diarrhea" by Da Silva et al.
"The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management" by Nabavi-Rad et al.
"The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept" by Sharon et al.
2023
"The emerging role of the small intestinal microbiota in human health and disease" by Ruigrok et al.
"Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial" by Corbin et al.
People
Today I found a paper that I really liked and saw the name of the author and of course it was very familiar in the world of microbiology. What I did not know it was that the author had a remarkable list of fascinating papers starting in 1978! Because of him (Willem de Vos), I decided to start a new section in this library about people that have dedicated part of their lives to study microorganisms in one way or another. The idea is not to make a biography of each person or to focus in any particular area but instead of focusing (litle by little) on the specific contributions of each person.
Antonie Philips van Leeuwenhoek (October 24 1632 - August 26 1723) was a Dutch businessman and the first acknowledged microscopist and microbiologist. He discovered microorganisms.
Christian Gottfried Ehrenberg (April 19 1795 - June 27 1876) was a German naturalist, zoologist, comparative anatomist, geologist, and microscopist. Apparently, he was the first to "discover" Bacillus subtilis and called it Vibrio subtilis (visit this website for more information about B. subtilis).
Louis Pasteur (December 27 1822 – September 28 1895) was a French biologist, microbiologist and chemist renowned for his discoveries of the principles of vaccination, microbial fermentation and pasteurization.
Ferdinand Julius Cohn (January 24 1828 - June 25 1898) was a German biologist. He is one of the founders of modern bacteriology and microbiology.
Emil Christian Hansen (May 8 1842 – August 27 1909) was a Danish mycologist and fermentation physiologist. Among many other things, in 1896 he published Practical Studies in Fermentation.
Elie Metchnikoff (May 3 1845 – July 15 1916) was a Russian zoologist best known for his pioneering research in immunology. He is also famous because of his work on the gastrointestinal microbiota.
Sergei Winogradsky (September 1 1856 - February 25 1953) was a Russian microbiologist, ecologist and soil scientist who pioneered the cycle-of-life concept.
Robert Hungate (March 2 1906 - September 21 2004) was a pioneering microbial ecologist who developed the first techniques for the culturing of anaerobic microbes in his study of the bovine rumen.
Carl Woese (July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. He got famous because he defined the realm of Archaea based on phylogenetic taxonomy using the 16S rRNA gene.
Norman R. Pace, born 1942. Among many other things, he has published several exciting papers on Microbial Ecology and evolution such as this paper.
George E. Fox, born December 17 1945. He and Carl Woese defined the Archaea as a separate domain. Fox and Woese also introduced the idea of a progenote as a primordial entity in the evolution of life.
Willem de Vos, born October 30 1954. He has published a wide variety of papers (>700 as for today) related to Bacteria and other microorganisms. Among many other things, Willem is famous because he won the Spinoza Prize (this award is the highest scientific award in the Netherlands, 2.5 million euros) in 2008. It is always a lot of fun to listen to his talks.
Rob Knight, born 1976, is an New Zelander that has published a wide variety of papers (>500 as for today), first on marvelous aspects of the genetic code, then on the Earth microbiome. Among many other things, Rob is the Chief Security Officer of Biota.
Notes and comments
"There were multiple sources of leavening available for early bread. Airborne yeasts could be harnessed by leaving uncooked dough exposed to air for some time before cooking". Bread in Wikipedia.
This is just a funny note but after decades of mentioning that we are 10 times more bacteria than human eukaryotic cells, finally someone decided to argue against this thought. You can read the discussion here. As far as I remember I have never mentioned this myth in my papers but even if it would be 10 times more bacteria, bacteria are 10 times smaller than our average cells so I was doubtful that the numbers would have any significance. This paper by Sender et al. (2016) provides more information about this.
I am making this note for myself in the future. Remember Paenibacillus for the beatiful colony growth (link)
Lumping versus splitting – is it time for microbial ecologists to abandon OTUs? Very interesting discussion from the Fierer Lab about an exciting topic in Microbial Ecology.
"The related sequences corresponded to a protein from the lens of eye from beef cattle, a protein from brain of Drosophila fruit flies, a protein that permits Escherichia coli to use glycerol as a carbon source, and a series of related proteins from various plant tissues" in The Aquaporin Water Channels by Peter Agre, refering to the very first DNA sequences from aquaporins from red cells.
"Imagínate que te digan que tienes 732 bacterias que horror!" platica con gente de la Oficina de Convenciones y Visitantes de Monterrey, Junio 12, 2019. El numero es interesante porque la persona que lo menciono no sabia nada de microorganismos. ¿Sera que cientos de microorganismos resulten realmente aterradores? ¿Que pensarían entonces al saber que existen millones de microorganismos en sus mucosas internas y externas?