October 16, 2019

Happy Wednesday! Today’s digest includes the human gut virome, microbiome recovery after antibiotics, and the fungi growing on museum skeletons. Enjoy!

Pregnancy and early life

The vaginal microbial communities of healthy expectant Brazilian mothers and its correlation with the newborn’s gut colonization – Dobbler – World Journal of Microbiology and Biotechnology

Human skin microbiome

In vitro Antimicrobial Activity of Acne Drugs Against Skin-Associated Bacteria – Blaskovich – Scientific Reports

Human gut microbiome

Review: The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific – Shkoporov – Cell Host & Microbe

Review: Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System – Yue – Microorganisms

Individualized recovery of gut microbial strains post antibiotics – Koo – npj Biofilms and Microbiomes

Animal experiments

Depletion of dietary aryl hydrocarbon receptor ligands alters microbiota composition and function – Brawner – Scientific Reports

Rat H1 parvovirus infection leads to alterations in gut microbiota – Xiang – Pathogens and Disease

Positive effect of an electrolyzed reduced water on gut permeability, fecal microbiota and liver in an animal model of Parkinson’s disease – Bordoni – PLoS One

The Sulfate-Reducing Microbial Communities and Meta-Analysis of Their Occurrence during Diseases of Small–Large Intestine Axis – Kushkevych – Journal of Clinical Medicine

Plant, root, and soil microbiome

Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities – Sengupta – Biogeosciences

Water and extremophile microbiome

Diversity, Distribution, and Ecology of Fungi in the Seasonal Snow of Antarctica – Menezes – Microorganisms

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process – Zhang – Environmental Microbiology

Built environment

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale – Valencia-Agami – Microorganisms

Increased loading leads to convergence of microbial communities and high methane yield in adapted anaerobic co-digesters – Wang – Water Research

Skeleton bones in museum indoor environments offer niches for fungi and are affected by weathering and deposition of secondary minerals – Pinzari – Environmental Microbiology


Species abundance information improves sequence taxonomy classification accuracy – Kaehler – Nature Communications

October 11, 2019

Good morning everyone!

Today’s digest is full of great reviews paper, among else- from the gut microbiome to bacterial metabolic modelling. Also featured is a lovely paper regarding vaginal microbiome transplantation (with interesting translational meaning!) and a food-for-thought paper about microbiology past, present and furture (1st in the list down).

Have a great weekend and happy Jewish New year!

Food for Thought

Shift in the paradigm towards next-generation microbiology, Blaz Sterz & Luka Kronegger, FEMS Microbiology Letters

Human microbiome

** Re‐assessing microbiomes in the low‐biomass reproductive niche, Jessica L. O’Callaghan, BJOG

** Incorporating functional trade-offs into studies of the gut microbiota, Aspen T Reese, Curr. Opi. Microbiology

** Gut microbial metabolites in depression: understanding the biochemical mechanisms, Giorigia Caspani, microbial cell

** Vaginal microbiome transplantation in women with intractable bacterial vaginosis, Ahinoam Lev-Sagie, Nature Medicine

Gut microbiome diversity is associated with sleep physiology in humans, Robert P. Smith, PLOS One

Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties, P.I. Diaz, J. Dental Research

Animal microbiome

A wild microbiome improves mouse modeling of the human immune response, Sara E. Hamiltion, Lab Animal

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability, Duy Le, Microbial Ecology

Environmental microbiome

** Implications of indoor microbial ecology and evolution on antibiotic resistance, Sarah Ben Maamar, J. Exp. science & Env. Epid.

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability, O. Nicolitch, Scientific Reports

Preceding crop and tillage system affect winter survival of wheat and the fungal communities on young wheat roots and in soil, Hanna Friberg, FEMS Microbiology Letters

Viral microbiome

A review on viral metagenomics in extreme environments, Sonia Davila-Ramos, Frontiers in Microbiology

Methods in microbiology

Multi-faceted approaches to discovering and predicting microbial nutritional interactions, Sebastian Gude, Curr. Opi. Biotechnology

Artificial neural network-assisted Fourier transform infrared spectroscopy for differentiation of Salmonella serogroups and its application on epidemiological tracing of Salmonella Bovismorbificans outbreak isolates from fresh sprouts, Helene Obereuter, FEMS Microbioogy Letters

October 9, 2019

Today’s Digest includes plenty of human gut microbiome papers, and plant, soil, water microbiome papers. Today features a major expansion of human gut MAGs, evolution of human gut microbiome compared with apes, and how soil microbiome affects climate change and vice versa. A potentially revolutionary technology promises to finally bring microbiome dark matters into daylight, and don’t forget to check out our own Elies Bik’s excellent work on exposing scientific fraud! Enjoy.

General microbiology

Tradeoffs in hyphal traits determine mycelium architecture in saprobic fungi – Anika Lehmann et al. – Scientific Reports

Review: Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction – Stephen P Lillington et al. – Current Opinion in Biotechnology

Review: Microbial functional diversity: From concepts to applications – Arthur Escalas e t al. – Ecology and Evolution

Antimicrobial resistance

Preprint: Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study – Ronan M Doyle et al. – bioRxiv

Human gut microbiome

** Preprint: A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome – Alexandre Almeida et al. – bioRxiv

** Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny – Katherine R. Amato et al. – Genome Biology

Press: New research furthers understanding about what shapes human gut microbiome – EurekAlert!

Review: Sodium, Hypertension, and the Gut: Does the Gut Microbiota Go Salty? – Katarina Smiljanec & Shannon L. Lennon – American Journal of Physiology-Heart and Circulatory Physiology

Tea Compounds and the Gut Microbiome: Findings from Trials and Mechanistic Studies – Timothy Bond & Emma Derbyshire – Nutrients

Fecal microbiota and metabolites are distinct in a pilot study of pediatric Crohn’s disease patients with higher levels of perceived stress – Laura M. Mackner et al. – Psychoneuroendocrinology

Review: The Gut Microbiota in Celiac Disease and probiotics – Richa Chibbar & Levinus A. Dieleman – Nutrients

Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? – Gregg J Silverman et al. – Current Opinion in Immunology

Review: The Multiple Sclerosis Gut Microbiota: A Systematic Review – Ali Mirza et al. – Multiple Sclerosis and Related Disorders

Animal experiments

Oolong tea polyphenols ameliorate circadian rhythm of intestinal microbiome and liver clock genes in mouse model – Tongtong Guo et al. – Journal of Agricultural and Food Chemistry

Review: Caenorhabditis elegans: a model to understand host–microbe interactions – Arun Kumar et al. – Cellular and Molecular Life Sciences

Animal microbiome

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales – Candace L. Williams et al. – Drug Discovery Today: Disease Models

Plant, root and soil microbiome

Soil Microbial Communities Involved in Reductive Dissolution of Arsenic from Arsenate-laden Minerals with Different Carbon Sources – Shigeki Yamamura et al. – Environmental Science & Technology

Volatile‐mediated antagonism of soil bacterial communities against fungi – Xiaogang Li et al. – Environmental Microbiology

Interactions between soybean, Bradyrhizobium japonicum and Soybean mosaic virus: the effects depend on the interaction sequence – Sofía Andreola et al. – Functional Plant Biology

New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics – Xiaona Li et al. – Environmental Pollution

Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures – Prashant Singh et al. – Scientific Reports

** Review: Soil microbiomes and climate change – Janet K. Jansson & Kirsten S. Hofmockel – Nature Reviews Microbiology

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Plant-plant competition influences temporal dynamism of soil microbial enzyme activity – E. J. Schofield et al. – Soil Biology and Biochemistry

Comparison of microphototrophic communities living in different soil environments in the High Arctic – Ekaterina Pushkareva et al. – Frontiers in Ecology and Evolution

Water and extremophile microbiome

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps – Muhammad Farhan Ul Haque et al. – Microbiome

Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site – Edoardo Puglisi et al. – Scientific Reports

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland) – Magdalena Dyda et al. – Microorganisms

Evaluating the effect of biochar on mesophilic anaerobic digestion of waste activated sludge and microbial diversity – Bo Wu et al. – Bioresource Technology

Species-specific differences in the microbiomes and organic exudates of crustose coralline algae influence bacterioplankton communities – Zachary A. Quinlan et al. – Frontiers in Microbiology

A global comparison of the bacterial communities of bilge water, boat surfaces, and external port water – Laura G. Schaerer et al. – Applied and Environmental Microbiology

Microbes in space

Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system – Hai-Sheng Dong et al. – PeerJ


** Targeted isolation and cultivation of uncultivated bacteria by reverse genomics – Karissa L. Cross et al. – Nature Biotechnology


Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases – Ole K Tørresen et al. – Nucleic Acids Research

Microbes in the news

Bill Gates thinks understanding the body’s microbiome will help solve malnutrition – Katie Palmer – Quartz

Press for yesterday’s article: Unlocking CRISPR’s Potential To Alter the Microbiome – Technology Networks

Press for yesterday’s article: New Study Finds CRISPR May Be The Secret To Improving Gut Health – Gretchen Lidicker – Mind Body Green

Drug Metabolism and Microbiome – Maryam Azizi – News Medical

The Gut-Lupus Link: How Gut Bacteria May Impact Disease Development and Activity – Lupus Foundation of America

Microbes on the market

BASF and Biomillenia Join Forces in Microbiome Research to Promote Healthy Skin – Business Wire

Non-microbiology pick

** Our own Elies Bik is featured in this Dutch report on exposing scientific fraud, and see a Google translated version here.

CRISPR-Cas9 system that kills targeted pathogenic bacteria may be microbiome friendly.

By: Puck deRoos

Please join me in welcoming our new contributor Puck deRoos. She will be writing short articles about the latest microbiome papers. I am so excited to have you on the team! – Elisabeth Bik

New research has highlighted a potential system that can specifically target pathogenic bacteria without disturbing the rest of the microbial community1.  

Currently, the ways to treat pathogenic bacterial infections are non-specific and may have unintentional longer lasting effects because they often alter the composition of the gut microbiome. The rise of multi-drug resistant bacteria has shown the limitations of general broad-spectrum antibiotics2, while phage-based therapy has been associated with  a smaller but similar rise in phage resistant bacteria3,.  Stool transplants have shown promising results in treatment of particular intestinal conditions, but are not suitable for many other diseases. In addition, they completely alter the patients gut microbiome, which may have unknown long-term effects4


The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas-9 (CRISPR ASsociated protein-9) system is able to target specific microbial species, and cause cell death due to double stranded breaks in the microbial DNA. In a recent paper published in Nature Communications, researchers have developed a method to specifically target microbial pathogens using a cis-conjugative CRISPR system where all the necessary machinery is encoded within one plasmid, or bacterial DNA sequence.

The cis-conjugative plasmid system has much higher rate of conjugation, which is how bacteria transfer genetic material between different cells, than its trans-conjugative counterpart, which has the CRISPR and conjugative sequences on different plasmids. One of the reasons the cis-conjugative system is more effective is that it is able to continue to work throughout multiple conjugations, so its effect increases exponentially throughout time. In contrast,  the trans system only works once. 

The rates of conjugation were measured from host bacteria Escherichia coli to bacterial recipient Salmonella enterica. The rate for the cis system continually increased and reached a maximum of 1 X 10-2 at 24hour, while the trans system maxed out early at ~1 X 10-3 but decreased to ~1 X 10-5 at 24hours. These results showed a ~1000-fold increase in the rates of the new cis-conjugative system compared to previous trans-conjugative system. 

Macintosh HD:Users:puck:Desktop:Screen Shot 2019-10-04 at 3.51.57 PM.png


This new tool for targeting specific bacteria can be extremely useful within the human microbiome. Most microbial communities in our body exists as a biofilm, a community of different microorganisms that stick together on a surface. The new cis-conjugative system developed by researchers at Schulich School of Medicine and Dentistry has up to a potential 100% effective rate of conjugation with bacteria grown in a biofilm. The same cis system in a regular bacterial assay or filter based assay shows a ~500 to 1000-fold decrease in the rate of conjugation, increasing the systems usefulness in regards to the microbiome. 

In conclusion, this new method of specifically delivering a CRISPR-Cas-9 system to pathogenic bacteria without disrupting the composition of the entire microbial community is an exciting new direction for the targeted  treatment of microbial infections. 


1. Hamilton TA et al. Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing. Nature Communications. 10, 4544 (2019). https://doi.org/10.1038/s41467-019-12448-3

2. Theuretzbacher, U. Antibiotic innovation for future public health needs. Clin. Microbiol. Infect. 23, 713–717 (2017). 

3. Chatain-Ly, M. H. The factors affecting effectiveness of treatment in phages therapy. Front. Microbiol. 5, 51 (2014). 

4. Khanna, S. et al. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. Microbiome 5, 55 (2017). 


October 7, 2019

Good Morning! Highlights of today’s digest include investigation about early childhood microbiota assembly in mother-infant participants from the Tsimane indigenous population from Amazon and with findings suggesting that socioeconomic changes may be altering interactions of highly abundant members of the microbiota in the host. Results from a gut-brain axis rat model showed possibility of novel biomarkers development for stress response based on abundance of genes in microbiomes. Finally, another study is aiming to access biologically active small molecules with antibacterial activity derived from human microbiota by sequencing of metagenomes and the use of computational and synthetic biology methods.

Pregnancy and early life
Prenatal and postnatal contributions of the maternal microbiome on offspring programming – Jasarevic and Bale – Frontiers in Neuroendocrinology

Multi-site human microbiome
*Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon – Sprockett et al. – bioRxiv

Human vaginal microbiome
Oncogenic Virome Benefits from the Different Vaginal Microbiome-Immune Axes – Campisciano et al. – MDPI Microorganisms

Non-optimal vaginal microbiota after azithromycin treatment for Chlamydia trachomatis infection – Tamarelle et al. – The Journal of Infectious Diseases

Human nearly-sterile sites
Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India – Gandhi et al. – MDPI Microorganisms

Human gut microbiome
Review: Synthetic ecology of the human gut microbiota – Vrancken et al. – Nature Reviews Microbiology

Review: The interaction between gut microbiome and nutrients on development of human disease through epigenetic mechanisms – Ho-Sun Lee – Genomics & Informatics

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity – Dejean et al. – Applied and Environmental Microbiology

Pre‐and post‐serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation – Kusakabe et al. – British Journal of Haematology

Animal experiments
Experimental evidence for adaptation to species-specific gut microbiota in house mice – Moeller et al. – mSphere

Low‐calcium diet in mice leads to reduced gut colonization by Enterococcus faecium – Top et al. – MicrobiologyOpen

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Arroyo et al. – PLOS ONE

Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice – Lin et al. – Frontiers in Cellular and Infection Microbiology

*Metabolome and microbiome profiling of a stress-sensitive rat model of gut-brain axis dysfunction – Bassett et al. – Nature Scientific Reports

Animal microbiome
The composition and stability of the faecal microbiota of Merino sheep – Al Mamun et al. – Journal of Applied Microbiology

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits – Fang et al. – Microbial Biotechnology

Review: Feline Virome—A Review of Novel Enteric Viruses Detected in Cats – Martino et al. – MDPI Viruses

Phylogeography and ecological niche shape the cichlid fish gut microbiota in Central American and African lakes – Baldo et al. – Frontiers in Microbiology

Plant, root and soil microbiome
Biocontrol activities of rhizobacteria associated with apple, apricot and kiwi rhizosphere against bacterial canker caused by Clavibacter michiganensis – Gautam et al. – Indian Phytopathology

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes – Zhang et al. – mSystems

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes – Oh et al. – Journal of Microbiology

Microbial communities in bioswale soils and their relationships to soil properties, plant species, and plant physiology – Brodsky et al. – Frontiers in Microbiology

Soil prokaryotes associated with decreasing pathogen density during anaerobic soil disinfestation – Lee et al. – bioRxiv

Water and extremophile microbiome
Bacterial Communities of Microbial Mats of the White Sea Supralittoral and of the Littoral of the Lakes Separated from the Sea – Burganskaya et al. – Microbiology

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom – Bhatnagar et al. – bioRxiv

*A metagenomic strategy for harnessing the chemical repertoire of the human microbiome – Sugimoto et al. – Science

Protocol: Open-Source Software Tools, Databases, and Resources for Single-Cell and Single-Cell-Type Metabolomics – Biswapriya B. Misra – Single Cell Metabolism

An Entropy-Based Graph Construction Method for Representing and Clustering Biological Data – Ariza-Jimenez et al. – Latin American Conference on Biomedical Engineering

Microbes in the news
Artificial gut aims to expose the elusive microbiome – Anne McGovern – MIT PHYS.ORG

October 5, 2019

This weekend, read about how cooking food modifies the microbiome, how bacteria ‘strip off’ to evade antibiotics, and more. Check out an interesting pilot study looking at potential inclusion and exclusion criteria of donors for safe vaginal microbiota transplant. Enjoy!


Bioinformatics for the Microbiome Symposium 2019, Stanford University, Monday October 28.
Some tickets are still available!

General microbiome

Mobile phones as fomites for potential pathogens in hospitals: microbiome analysis reveals hidden contaminants – Rebecca Simmonds – Journal of Hospital Infection

Review: Microbiomes as sources of emergent host phenotypes – J. B. Lynch and E. Y. Hsiao – Science

Vaginal microbiome

*Conceptual Design of a Universal Donor Screening Approach for Vaginal Microbiota Transplant – Kevin DeLong – Frontiers in Cellular and Infection Microbiology

Highly diverse anaerobe-predominant vaginal microbiota among HIV-infected pregnant women in Zambia – Joan T. Price – PlosOne

Urinary microbiome

*Possible role of L-form switching in recurrent urinary tract infection – Katarzyna M. Mickiewicz – Nature Communications

Aerococcus urinae and Globicatella sanguinis Persist in Polymicrobial Urethral Catheter Biofilms Examined in Longitudinal Profiles at the Proteomic Level – Yanbao Yu – Biochemistry Insights

Gut microbiome

*Cooking shapes the structure and function of the gut microbiome – Rachel N. Carmody – Nature Microbiology

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma – Wen Fong Ooi – Gut

Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial – Selina R.Cox – Gastroenterology

Water microbiome

Trophic networks improve the performance of microbial anodes treating wastewater – Christin Koch – npj Biofilms and Microbiomes

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge – Luong N.Nguyen – Journal of Environmental Management

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus – Ragnhildur Guðmundsdóttir – PlosOne

Animal microbiome

Looking like the locals – gut microbiome changes post-release in an endangered species – Rowena Chong – Animal microbiome

Animal experiment

Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome – Pablo Arroyo – PlosOne

Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection – Ashley D. Smith – PlosOne

Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model – Yoshitomo Morinaga – PlosOne

Plant microbiome

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae) – Suresh J. Gawande – PlosOne


Comparison of the microbial composition of African fermented foods using amplicon sequencing – Maria Diaz – Scientific Reports

The impact of grape processing and carbonic maceration on the microbiota of early stages of winemaking – Raffaele Guzzon – Journal of Applied Microbiology


Phyllosphere Fungal Communities of Plum and Antifungal Activity of Indigenous Phenazine-Producing Pseudomonas synxantha Against Monilinia laxa – Tamara Janakiev – Frontiers in Microbiology

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses – Gian Maria Niccolò Benucci – PeerJ


The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches – Federica Ungaro – United European Gastroenterology Journal

Association of the Eukaryotic Vaginal Virome with Prophylactic Antibiotic Exposure and Reproductive Outcomes in a Subfertile Population Undergoing In Vitro Fertilization: A Prospective Exploratory Study – Ashley M. Eskew – Obstetrics and Gynaecology


ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database – João L. Reis-Cunha – PlosOne

The Hetch Hetchy Railroad

This post has nothing to do with microbiology, but everything with my love for maps. It is about the former Hetch Hetchy Railroad.

Hetch Hetchy reservoir is the main source of drinking water for the city of San Francisco and other parts of the Bay Area. The densely populated SF Bay Area only gets rainfall in the winter months and is dependent on reservoirs in the Sierra Nevada mountains for the collection and storage of rain and melting snow water for the dry summer months.

The Hetch Hetchy area once was a glacier-formed valley of what is now Yosemite National Park, California. It is located in the Northwestern part of the national park, far away from the much more famous Yosemite Valley. Hetch Hetchy Valley was equally beautiful, but it was turned into a reservoir, an artificial lake, in 1923 upon the completion of the O’Shaughnessy Dam.

O’Shaughnessy Dam at Hetch Hetchy reservoir. Photo by Inklein at English Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=8256821

Here are two photos comparing Hetch Hetchy valley before and after the dam was completed, taken from roughly the same position.

Screen Shot 2019-07-24 at 5.52.04 PM.png

Top: Hetch Hetchy Valley in the early 1900, with the Tuolumne River. Source: Isaiah West Taber – Sierra Club Bulletin, Vol. VI. No. 4, January, 1908, pg. 211 (Wikipedia). Bottom: Hetch Hetchy reservoir, May 2002. Photo by Daniel Mayer. Source: Wikipedia.

As of today, the Hetch Hetchy Project consists of the reservoir, the dam, hydroelectric plants, and a long aqueduct that carries the water to the SF Bay Area through a long series of tunnels, using only gravity.


Hetch Hetchy Project. Source: By Shannon1 using Adobe Illustrator CS5; aqueduct path data from USGS topos, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=26434757.

The story about the Hetch Hetchy Railroad, built in the 1910s and 1920s to bring the construction crews and materials needed to build the dam, hydroelectric plants, and aqueducts is very interesting if you like history and maps. After completion of the dam in 1923, the HHRR was used to carry tourists and mail to the Northern Yosemite area. However, the steep terrain, sharp curves, and heavy snowfall made it very hard and expensive to operate the railroad. During World War II, HHRR rail materials such as steel and wood were used for war operations, and the railroad was finally completely dismantled in 1949.

Hetch Hetchy Railroad Locomotive #2 in the Travel Town Museum in Los Angeles, 2017. Photo by NearEMPTiness, Wikipedia.com

Friends of us who live near an area where the railroad used to run told us about the success and decline of the railroad, and pointed us towards some sections where you can still see remnants of how the tracks ran. Even though the rails and wooden cross-ties are now all gone, you can still see the flattened track at some sections. Close to the Hetch Hetchy reservoir, the road to access the lake now runs over the railroad track.

Online maps and photos of the Hetch Hetchy Railroad

Hearing about the now-gone railroad got me interested in mapping the complete course of the railroad. I first searched online and found a couple of railroad and other sites that mentioned it.

  • GhostRails and AbandonedRails (very similar sites) both have a rough map of the first part of the route and some discussion on where to see remnants of the railway
  • San Francisco’s Municipal Transportation Agency has a site that remembers how San Franciscans could take the railway up to the Hetch Hetchy reservoir to visit the site where their drinking water came from and see their tax dollars at work.
  • MTB project has a bike route that follows part of the track around Groveland
  • Wikipedia has a page that describes when the railroad was in operation and which locomotives ran over it. It also describes how steep and curvy the track was.
  • Latitude.to has the GPS coordinates of the start of the track, in California’s Central Valley west of the Don Pedro Reservoir, at Hetch Hetchy Junction
  • There is also a Hetch Hetchy Railroad museum in El Portal, west of Yosemite National Park’s entrance on Highway 140
  • Several old maps were also available online, such as this map at Yosemite News. On the map below,  you can see that it split off from the (still-existing) Sierra Railroad.

Map from 1947 displaying the Hetch Hetchy Railroad

More maps and information about the HH Railroad

The information I found online was not enough detailed to know how the HHRR exactly ran. Luckily, our friends lent us their copy of the book Yosemite’s Hetch Hetchy Railroad by Ted Wurm. The author was part of a group of railfans who traveled the railroad around 1937 and took lots of photos. This book has a map of the railroad route, and several descriptions that allowed me to start to map the exact position of the tracks.

Photo of Ted Wurm's book about the Hetch Hetchy Railroad

Yosemite’s Hetch Hetchy Railroad by Ted Wurm

The Groveland Yosemite Gateway Museum also has a small exhibition on the Hetch Hetchy Railroad. It consists of several photos and a topographical map in which a person called Bill Dagg draw the course of the railroad by hand.

Map of the HHRR in the Groveland Museum, hand-drawn by Bill Dagg

Drawing the exact location of the railroad in Google Earth

These two maps by Ted Wurm and Bill Dagg were a lot more detailed than what I could find online. I was very excited to see how much work these two men had put into mapping the railroad.

Since I could not find an electronic version of the railroad’s course online, I decided to make a KML file myself. KML stands for “Keyhole Markup Language“, and is a way to visualize geographic data in – for example – Google Earth. Google Earth is the advanced version of Google Maps and it allows you to add extra layers. An easy way to make a KML file is to draw a line or a polygon on top of the map displayed in Google Earth.

In order to draw the map, I downloaded Google Earth Pro. There is also a Google Earth Web version that runs in Chrome and that can display KML files, but it did not allow me to make one or edit points.

Using Google Earth satellite views and the maps from Ted Wurm’s book and Bill Dagg’s map from the Groveland Museum it was easy to spot some parts of the now-dismantled railroad. In some places, the railroad is now an unpaved or paved road, while in other spots the old foundations are still visible in the landscape.

Google Maps satellite view of the western-most part of the Hetch Hetchy Railroad. The leftmost and rightmost arrows show visible remnants of the track foundations, while the other arrows show parts that now serve as a road.

I was also very excited to find some historical topographical maps on the website of the USGS from around 1947, just before the railroad was removed. These maps are available as KMZ (zipped KML) files, so you can just overlay them in Google Earth. This allowed me to draw the railroad even more precisely.

Historical topographic map from USGS as a KMZ overlay in Google Earth. The red line is my drawing of the railroad.

This was a fun project to do in Google Earth. In some cases, the historic topographical maps were a bit shifted from the current Google map, and in other cases new roads were put over the historic railroad, so I had to make an educated guess where the tracks had been. But in most spots it was easy to see the old tracks from the satellite images.

Download the Hetch Hetchy Railroad

So here it is, a link to the historic Hetch Hetchy Railroad route (KML file) as drawn by me in Google Earth. If you click on the link it will show you the route in Google Maps.

Or, if you want to edit, download the KMZ file to display in Google Earth. Enjoy!

The Hetch Hetchy Railroad, mapped by Elisabeth Bik

One thing that struck me as amazing is how beautiful the incline of the trail is over certain areas. Look at this elevation profile that Google Earth draw over the complete 68-mile route. In several places, the tracks go up or down a nearly perfect 4 degrees. What a great piece of 1920s engineering that was!

Elevation profile of the Hetch Hetchy Railroad, generated by Google Earth.